From owner-chemistry@ccl.net Sat Feb 5 04:55:01 2011 From: "Serdar Bado?lu sbadoglu*|*gazi.edu.tr" To: CCL Subject: CCL: generate electrostatic potential map problem in Gaussian Message-Id: <-43873-110205045318-2170-NqlbW7MN85srHBY35BpeTg]~[server.ccl.net> X-Original-From: "Serdar Bado?lu" Content-Type: text/plain; charset="iso-8859-9" Date: Sat, 5 Feb 2011 09:50:14 -0000 Sent to CCL by: "Serdar Bado?lu" [sbadoglu*gazi.edu.tr] Hi Hao, I have no idea about how to solve your problem. What I know is, there should be no limitations on number of atoms in the molecule. A couple of months ago I have been created ESP map of my molecule for my thesis, and the structure I've worked on has 28 atoms. Regards. -- Serdar BADOGLU Gazi University Department of Physics From owner-chemistry@ccl.net Sat Feb 5 06:17:00 2011 From: "sadia zafar diya.khan.05 ~~ gmail.com" To: CCL Subject: CCL: problem in running configuration file using NAMD Message-Id: <-43874-110205061609-22645-4Tp7HZ5ilwgcBnFeeMA/3g[]server.ccl.net> X-Original-From: sadia zafar Content-Type: multipart/alternative; boundary=00148539328cbbb327049b871fb3 Date: Sat, 5 Feb 2011 16:16:02 +0500 MIME-Version: 1.0 Sent to CCL by: sadia zafar [diya.khan.05__gmail.com] --00148539328cbbb327049b871fb3 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi, Thanks for your kind response sir. I am using NAMD for the very first time, therefore encountering some problems. You are rite. I was told by one of the NAMD users that the configuration file with default settings (placed in the NAMD tutorial example files) can be used as a standard file without making any change in it. Can you please guide me that how can i equilibrate my MD? What steps do I need to add up in my configuration file for the maintenance of my MD? On Fri, Feb 4, 2011 at 10:04 PM, Vincent Leroux vincent.lerouxa/loria.fr < owner-chemistry:ccl.net> wrote: > > Sent to CCL by: Vincent Leroux [vincent.leroux---loria.fr] > Hi, > > Look at the bottom of the parameter file. What you have been doing is: > - 100 minimization steps > - assign velocities for 302 K all of a sudden > - 2500 steps of MD > > 100 steps of minimization is probably not enough, but this is not the > problem. You just go straight from minimization to MD: MD is started with= a > random set of velocities averaged to T =3D 302 K, resulting in your syste= m > being literally torn apart. The RATTLE algorithm tries to compensate for > abnormal bond lengths occurring at the very first MD step, but of course = it > fails. > > You should do some equilibration after minimization... The comment at the > beginning of your parameter file is mistaking: it says "minimization and > equilibration" and below I see the (right) comment "do langevin dynamics"= . > Seems like this input file was messed up by careless copy-paste operation= s. > > Regards > VL > > > > Le 04/02/11 06:59, neha khan diya.khan.05(~)gmail.com a =E9crit : > > Sent to CCL by: "neha khan" [diya.khan.05~~gmail.com] >> Respected Sir, >> When i run minimization, the program stopped abnormally. What is wrong >> with my file? >> >> REINITIALIZING VELOCITIES AT STEP 100 TO 302 KELVIN. >> TCL: Running for 2500 steps >> ERROR: Constraint failure in RATTLE algorithm for atom 2775! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Constraint failure in RATTLE algorithm for atom 2729! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Constraint failure in RATTLE algorithm for atom 1739! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Constraint failure in RATTLE algorithm for atom 2926! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Constraint failure in RATTLE algorithm for atom 6029! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Constraint failure in RATTLE algorithm for atom 2398! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Constraint failure in RATTLE algorithm for atom 2202! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Constraint failure in RATTLE algorithm for atom 3201! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Constraint failure in RATTLE algorithm for atom 5028! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Constraint failure in RATTLE algorithm for atom 2390! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Constraint failure in RATTLE algorithm for atom 553! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Constraint failure in RATTLE algorithm for atom 3136! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Constraint failure in RATTLE algorithm for atom 4966! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Constraint failure in RATTLE algorithm for atom 1588! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Constraint failure in RATTLE algorithm for atom 4118! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Constraint failure in RATTLE algorithm for atom 1275! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Constraint failure in RATTLE algorithm for atom 771! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Constraint failure in RATTLE algorithm for atom 1069! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Constraint failure in RATTLE algorithm for atom 4008! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Constraint failure in RATTLE algorithm for atom 867! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Constraint failure in RATTLE algorithm for atom 919! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Constraint failure in RATTLE algorithm for atom 3447! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Constraint failure in RATTLE algorithm for atom 6355! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Constraint failure in RATTLE algorithm for atom 4747! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Constraint failure in RATTLE algorithm for atom 332! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Constraint failure in RATTLE algorithm for atom 6837! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Constraint failure in RATTLE algorithm for atom 82! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Constraint failure in RATTLE algorithm for atom 1542! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Constraint failure in RATTLE algorithm for atom 1254! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Constraint failure in RATTLE algorithm for atom 9773! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Constraint failure in RATTLE algorithm for atom 1193! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Constraint failure in RATTLE algorithm for atom 3739! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Constraint failure in RATTLE algorithm for atom 9465! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Constraint failure in RATTLE algorithm for atom 953! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Constraint failure in RATTLE algorithm for atom 10527! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Constraint failure in RATTLE algorithm for atom 3678! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Constraint failure in RATTLE algorithm for atom 117! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Constraint failure in RATTLE algorithm for atom 8745! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Constraint failure in RATTLE algorithm for atom 9881! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Constraint failure in RATTLE algorithm for atom 10838! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Constraint failure in RATTLE algorithm for atom 7839! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Constraint failure in RATTLE algorithm for atom 8262! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Constraint failure in RATTLE algorithm for atom 9955! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Constraint failure in RATTLE algorithm for atom 10206! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Constraint failure in RATTLE algorithm for atom 8881! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Constraint failure in RATTLE algorithm for atom 10080! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Constraint failure in RATTLE algorithm for atom 8404! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Constraint failure in RATTLE algorithm for atom 8589! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Constraint failure in RATTLE algorithm for atom 8450! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Constraint failure in RATTLE algorithm for atom 8308! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Constraint failure in RATTLE algorithm for atom 8580! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Constraint failure in RATTLE algorithm for atom 8572! >> ERROR: Constraint failure; simulation has become unstable. >> ERROR: Exiting prematurely; see error messages above. >> =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D >> >> WallClock: 74.289345 CPUTime: 74.199997 Memory: 99.713013 MB >> Program finished. >> execve failed to start process "namd2" with status: -1 >> execve failed to start process "namd2" with status: -1 >> execve failed to start process "namd2" with status: -1 >> execve failed to start process "namd2" with status: -1 >> Killed >> >> Below is my configuration file: >> >> >> ############################################################# >> ## JOB DESCRIPTION ## >> ############################################################# >> >> # Minimization and Equilibration of >> # pgl in a Water Sphere >> >> >> ############################################################# >> ## ADJUSTABLE PARAMETERS ## >> ############################################################# >> >> structure ../common/pgl_ws.psf >> coordinates ../common/pgl_ws.pdb >> >> set temperature 302 >> set outputname pgl_ws_eq >> >> firsttimestep 0 >> >> >> ############################################################# >> ## SIMULATION PARAMETERS ## >> ############################################################# >> >> # Input >> paraTypeCharmm on >> parameters ../common/par_all27_prot_lipid.inp >> temperature $temperature >> >> >> # Force-Field Parameters >> exclude scaled1-4 >> 1-4scaling 1.0 >> cutoff 12. >> switching on >> switchdist 10. >> pairlistdist 13.5 >> >> >> # Integrator Parameters >> timestep 2.0 ;# 2fs/step >> rigidBonds all ;# needed for 2fs steps >> nonbondedFreq 1 >> fullElectFrequency 2 >> stepspercycle 10 >> >> >> # Constant Temperature Control >> langevin on ;# do langevin dynamics >> langevinDamping 5 ;# damping coefficient (gamma) of 5/ps >> langevinTemp $temperature >> langevinHydrogen off ;# don't couple langevin bath to hydrogens >> >> >> # Output >> outputName $outputname >> >> restartfreq 500 ;# 500steps =3D every 1ps >> dcdfreq 250 >> outputEnergies 100 >> outputPressure 100 >> >> >> ############################################################# >> ## EXTRA PARAMETERS ## >> ############################################################# >> >> # Spherical boundary conditions >> sphericalBC on >> sphericalBCcenter 30.3081743413, 28.8049907121, 15.353994423 >> sphericalBCr1 26.0 >> sphericalBCk1 10 >> sphericalBCexp1 2 >> >> >> ############################################################# >> ## EXECUTION SCRIPT ## >> ############################################################# >> >> # Minimization >> minimize 100 >> reinitvels $temperature >> >> run 2500 ;# 5ps> >> >> >> > > > -=3D This is automatically added to each message by the mailing script = =3D-http://www.ccl.net/chemistry/sub_unsub.shtmlConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > --00148539328cbbb327049b871fb3 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi,
Thanks for your kind response sir.
I am using NAMD for th= e very first time, therefore encountering some problems. You are rite. I wa= s told by one of the NAMD users that the configuration file with default se= ttings (placed in the NAMD tutorial example files) can be used as a standar= d file without making any change in it.=A0
Can you please guide me that how can i equilibrate my MD? What steps d= o I need to add up =A0in my configuration file for the=A0maintenance=A0of m= y MD?=A0

On Fri, Feb 4, 2011 at 10= :04 PM, Vincent Leroux vincent.lerouxa/loria.fr= <owner= -chemistry:ccl.net> wrote:

Sent to CCL by: Vincent Leroux [vincent.leroux---loria.fr]
Hi,

Look at the bottom of the parameter file. What you have been doing is:
- 100 minimization steps
- assign velocities for 302 K all of a sudden
- 2500 steps of MD

100 steps of minimization is probably not enough, but this is not the probl= em. You just go straight from minimization to MD: MD is started with a rand= om set of velocities averaged to T =3D 302 K, resulting in your system bein= g literally torn apart. The RATTLE algorithm tries to compensate for abnorm= al bond lengths occurring at the very first MD step, but of course it fails= .

You should do some equilibration after minimization... The comment at the b= eginning of your parameter file is mistaking: it says "minimization an= d equilibration" and below I see the (right) comment "do langevin= dynamics". Seems like this input file was messed up by careless copy-= paste operations.

Regards
VL



Le 04/02/11 06:59, neha khan diya.khan.05(~)gmail.com a =E9crit :
=
Sent to CCL by: "neha =A0khan" [diya.khan.05~~gmail.com]
Respected Sir,
When i run minimization, the program stopped abnormally. What is wrong with= my file?

REINITIALIZING VELOCITIES AT STEP 100 TO 302 KELVIN.
TCL: Running for 2500 steps
ERROR: Constraint failure in RATTLE algorithm for atom 2775!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 2729!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 1739!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 2926!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 6029!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 2398!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 2202!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 3201!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 5028!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 2390!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 553!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 3136!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 4966!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 1588!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 4118!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 1275!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 771!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 1069!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 4008!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 867!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 919!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 3447!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 6355!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 4747!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 332!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 6837!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 82!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 1542!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 1254!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 9773!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 1193!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 3739!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 9465!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 953!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 10527!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 3678!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 117!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 8745!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 9881!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 10838!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 7839!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 8262!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 9955!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 10206!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 8881!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 10080!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 8404!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 8589!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 8450!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 8308!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 8580!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 8572!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Exiting prematurely; see error messages above.
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D

WallClock: 74.289345 =A0CPUTime: 74.199997 =A0Memory: 99.713013 MB
Program finished.
execve failed to start process "namd2" with status: -1
execve failed to start process "namd2" with status: -1
execve failed to start process "namd2" with status: -1
execve failed to start process "namd2" with status: -1
Killed

Below is my configuration file:


#############################################################
## JOB DESCRIPTION =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A0 =A0 ##
#############################################################

# Minimization and Equilibration of
# pgl in a Water Sphere


#############################################################
## ADJUSTABLE PARAMETERS =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A0 ##
#############################################################

structure =A0 =A0 =A0 =A0 =A0../common/pgl_ws.psf
coordinates =A0 =A0 =A0 =A0../common/pgl_ws.pdb

set temperature =A0 =A0302
set outputname =A0 =A0 pgl_ws_eq

firsttimestep =A0 =A0 =A00


#############################################################
## SIMULATION PARAMETERS =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A0 ##
#############################################################

# Input
paraTypeCharmm =A0 =A0 =A0on
parameters =A0 =A0 =A0 =A0 =A0../common/par_all27_prot_lipid.inp
temperature =A0 =A0 =A0 =A0 $temperature


# Force-Field Parameters
exclude =A0 =A0 =A0 =A0 =A0 =A0 scaled1-4
1-4scaling =A0 =A0 =A0 =A0 =A01.0
cutoff =A0 =A0 =A0 =A0 =A0 =A0 =A012.
switching =A0 =A0 =A0 =A0 =A0 on
switchdist =A0 =A0 =A0 =A0 =A010.
pairlistdist =A0 =A0 =A0 =A013.5


# Integrator Parameters
timestep =A0 =A0 =A0 =A0 =A0 =A02.0 =A0;# 2fs/step
rigidBonds =A0 =A0 =A0 =A0 =A0all =A0;# needed for 2fs steps
nonbondedFreq =A0 =A0 =A0 1
fullElectFrequency =A02
stepspercycle =A0 =A0 =A0 10


# Constant Temperature Control
langevin =A0 =A0 =A0 =A0 =A0 =A0on =A0 =A0;# do langevin dynamics
langevinDamping =A0 =A0 5 =A0 =A0 ;# damping coefficient (gamma) of 5/ps langevinTemp =A0 =A0 =A0 =A0$temperature
langevinHydrogen =A0 =A0off =A0 =A0;# don't couple langevin bath to hyd= rogens


# Output
outputName =A0 =A0 =A0 =A0 =A0$outputname

restartfreq =A0 =A0 =A0 =A0 500 =A0 =A0 ;# 500steps =3D every 1ps
dcdfreq =A0 =A0 =A0 =A0 =A0 =A0 250
outputEnergies =A0 =A0 =A0100
outputPressure =A0 =A0 =A0100


#############################################################
## EXTRA PARAMETERS =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0= =A0 =A0 =A0 =A0 =A0 =A0##
#############################################################

# Spherical boundary conditions
sphericalBC =A0 =A0 =A0 =A0 on
sphericalBCcenter =A0 30.3081743413, 28.8049907121, 15.353994423
sphericalBCr1 =A0 =A0 =A0 26.0
sphericalBCk1 =A0 =A0 =A0 10
sphericalBCexp1 =A0 =A0 2


#############################################################
## EXECUTION SCRIPT =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0= =A0 =A0 =A0 =A0 =A0 =A0##
#############################################################

# Minimization
minimize =A0 =A0 =A0 =A0 =A0 =A0100
reinitvels =A0 =A0 =A0 =A0 =A0$temperature

run 2500 ;# 5ps>





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--00148539328cbbb327049b871fb3-- From owner-chemistry@ccl.net Sat Feb 5 10:56:01 2011 From: "Vincent Leroux vincent.leroux[-]loria.fr" To: CCL Subject: CCL: problem in running configuration file using NAMD Message-Id: <-43875-110205104734-11705-R0KHU4pzMwOlgk/OYlGfDA:-:server.ccl.net> X-Original-From: Vincent Leroux Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Sat, 05 Feb 2011 16:47:22 +0100 MIME-Version: 1.0 Sent to CCL by: Vincent Leroux [vincent.leroux- -loria.fr] Hi, First of all you should write NAMD configuration files that perform a single task - this is much easier to understand and maintain. Typically you start from all-round files minimization.namd, equilibration.namd and dynamics.namd. "Multiple purpose" parameter files ending with an "execution script" phase are IMHO a really bad idea. In addition to visual inspection e.g. with VMD, you should check after minimization that there is no red light > from the log file, and make sure after equilibration that the system is actually equilibrated (stable energy, pressure, box size etc.). If you do not do that systematically you might be wasting valuable computational time. Then, tuning up the parameters depends on what kind of system you have... Usually, the better the quality of the starting model, the easier/shorter the minimization and equilibration. Check scientific publications to see what others are doing (you will quickly notice there are some conventions). Here are some sensible starting points - I do not mention parameters regarding trajectory recording, forcefield, electrostatics, PBC etc., this is just to highlight the differences between minimization, equilibration and dynamics with NAMD. The number of steps correspond to typical values for simulating medium-sized proteins in explicit solvent. Check the NAMD manual for explanations of the parameters, and description of many alternate methods. # minimization.namd structure start.psf coordinates start.pdb outputName minimized fixedAtoms on fixedAtomsForces on fixedAtomsCol B # start.pdb B column: 0->free 10->fixed minimization on # other related parameters defaults usually ok numSteps 5000 # equilibration.namd # Berendstein's method - temperature assignment/rescaling structure start.psf coordinates start.pdb # not taken into account binCoordinates minimized.coor # this one instead extendedSystem minimized.xsc outputname equilibrated berendsenPressure on berendsenPressureTarget 1.01325 # atmospheric pressure berendsenPressureCompressibility 4.57e-5 # liquid water berendsenPressureRelaxationTime 100.0 berendsenPressureFreq 10 temperature 0.5 # starting at 0.5 K reassignFreq 100 reassignIncr 0.5 reassignHold 300 # target T: 300 K numsteps 100000 # 100 ps, constant T the last 40 ps # dynamics.namd # NPT ensemble using Nose-Hoover Langevin piston structure start.psf coordinates start.pdb # not taken into account binCoordinates equilibrated.coor binVelocities equilibrated.vel # corresponds to T = 300 K extendedSystem equilibrated.xsc outputname dyn1-out LangevinPiston on LangevinPistonPeriod 100.0 LangevinPistonDecay 50.0 LangevinPistonTarget 1.01325 # constant pressure LangevinPistonTemp 300 # constant temperature numsteps 10000000 # 10 ns MD Hope it helps. You really have to understand the meaning and purpose of each single line of your parameter files, or you will have surprises later. If someone just tells you "just copy that standard parameter file > from wherever, it will work", don't you think this is too good to be true? ;-) Regards VL Le 05/02/11 12:16, sadia zafar diya.khan.05 ~~ gmail.com a écrit : > Hi, > Thanks for your kind response sir. > I am using NAMD for the very first time, therefore encountering some > problems. You are rite. I was told by one of the NAMD users that the > configuration file with default settings (placed in the NAMD tutorial > example files) can be used as a standard file without making any change > in it. > Can you please guide me that how can i equilibrate my MD? What steps do > I need to add up in my configuration file for the maintenance of my MD? > > On Fri, Feb 4, 2011 at 10:04 PM, Vincent Leroux vincent.lerouxa/loria.fr > > wrote: > > > Sent to CCL by: Vincent Leroux [vincent.leroux---loria.fr > ] > Hi, > > Look at the bottom of the parameter file. What you have been doing is: > - 100 minimization steps > - assign velocities for 302 K all of a sudden > - 2500 steps of MD > > 100 steps of minimization is probably not enough, but this is not > the problem. You just go straight from minimization to MD: MD is > started with a random set of velocities averaged to T = 302 K, > resulting in your system being literally torn apart. The RATTLE > algorithm tries to compensate for abnormal bond lengths occurring at > the very first MD step, but of course it fails. > > You should do some equilibration after minimization... The comment > at the beginning of your parameter file is mistaking: it says > "minimization and equilibration" and below I see the (right) comment > "do langevin dynamics". Seems like this input file was messed up by > careless copy-paste operations. > > Regards > VL > > > > Le 04/02/11 06:59, neha khan diya.khan.05(~)gmail.com > a écrit : > > Sent to CCL by: "neha khan" [diya.khan.05~~gmail.com > ] > Respected Sir, > When i run minimization, the program stopped abnormally. What is > wrong with my file? > > REINITIALIZING VELOCITIES AT STEP 100 TO 302 KELVIN. > TCL: Running for 2500 steps > ERROR: Constraint failure in RATTLE algorithm for atom 2775! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 2729! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 1739! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 2926! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 6029! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 2398! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 2202! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 3201! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 5028! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 2390! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 553! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 3136! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 4966! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 1588! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 4118! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 1275! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 771! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 1069! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 4008! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 867! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 919! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 3447! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 6355! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 4747! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 332! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 6837! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 82! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 1542! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 1254! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 9773! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 1193! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 3739! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 9465! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 953! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 10527! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 3678! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 117! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 8745! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 9881! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 10838! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 7839! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 8262! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 9955! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 10206! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 8881! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 10080! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 8404! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 8589! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 8450! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 8308! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 8580! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Constraint failure in RATTLE algorithm for atom 8572! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Exiting prematurely; see error messages above. > ==================================================== > > WallClock: 74.289345 CPUTime: 74.199997 Memory: 99.713013 MB > Program finished. > execve failed to start process "namd2" with status: -1 > execve failed to start process "namd2" with status: -1 > execve failed to start process "namd2" with status: -1 > execve failed to start process "namd2" with status: -1 > Killed > > Below is my configuration file: > > > ############################################################# > ## JOB DESCRIPTION ## > ############################################################# > > # Minimization and Equilibration of > # pgl in a Water Sphere > > > ############################################################# > ## ADJUSTABLE PARAMETERS ## > ############################################################# > > structure ../common/pgl_ws.psf > coordinates ../common/pgl_ws.pdb > > set temperature 302 > set outputname pgl_ws_eq > > firsttimestep 0 > > > ############################################################# > ## SIMULATION PARAMETERS ## > ############################################################# > > # Input > paraTypeCharmm on > parameters ../common/par_all27_prot_lipid.inp > temperature $temperature > > > # Force-Field Parameters > exclude scaled1-4 > 1-4scaling 1.0 > cutoff 12. > switching on > switchdist 10. > pairlistdist 13.5 > > > # Integrator Parameters > timestep 2.0 ;# 2fs/step > rigidBonds all ;# needed for 2fs steps > nonbondedFreq 1 > fullElectFrequency 2 > stepspercycle 10 > > > # Constant Temperature Control > langevin on ;# do langevin dynamics > langevinDamping 5 ;# damping coefficient (gamma) of 5/ps > langevinTemp $temperature > langevinHydrogen off ;# don't couple langevin bath to > hydrogens > > > # Output > outputName $outputname > > restartfreq 500 ;# 500steps = every 1ps > dcdfreq 250 > outputEnergies 100 > outputPressure 100 > > > ############################################################# > ## EXTRA PARAMETERS ## > ############################################################# > > # Spherical boundary conditions > sphericalBC on > sphericalBCcenter 30.3081743413, 28.8049907121, 15.353994423 > sphericalBCr1 26.0 > sphericalBCk1 10 > sphericalBCexp1 2 > > > ############################################################# > ## EXECUTION SCRIPT ## > ############################################################# > > # Minimization > minimize 100 > reinitvels $temperature > > run 2500 ;# 5ps> > > > E-mail to subscribers: CHEMISTRY=-=ccl.net > or use:> > E-mail to administrators: CHEMISTRY-REQUEST=-=ccl.net > or useConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > From owner-chemistry@ccl.net Sat Feb 5 11:40:00 2011 From: "Egon Willighagen egon.willighagen#%#gmail.com" To: CCL Subject: CCL: Large .XYZ file visualization Message-Id: <-43876-110205050701-2768-3nskBZiF2OBv/GFZo8175Q[a]server.ccl.net> X-Original-From: Egon Willighagen Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Sat, 5 Feb 2011 10:06:33 +0000 MIME-Version: 1.0 Sent to CCL by: Egon Willighagen [egon.willighagen_+_gmail.com] Dear Alex, On Wed, Feb 2, 2011 at 12:59 PM, Alex Naden anaden],[fsmail.net wrote: > Could anyone recommend a software (Linux/ Windows) or on-line that is capable of handling very large .xyz files? Please have a look at Jmol. We ran some simple analysis some years ago [0], and found that a 2.2 GHz Athlon with 1GB machine would render a 500x500 pixels a membrane of 40k atoms at 17 FPS, and a rhino virus with 393k atoms at 2 FPS. Hoping this helps, Egon 0.Willighagen, E. and Howard, M. Fast and Scriptable Molecular Graphics in Web Browsers without Java3D. Available from Nature Precedings (2007) -- Dr E.L. Willighagen Postdoctoral Researcher Institutet för miljömedicin Karolinska Institutet Homepage: http://egonw.github.com/ LinkedIn: http://se.linkedin.com/in/egonw Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers From owner-chemistry@ccl.net Sat Feb 5 16:34:00 2011 From: "James Womack james.c.womack_._gmail.com" To: CCL Subject: CCL: Molpro execution problem in Ubuntu 10.04 Message-Id: <-43877-110205120604-4563-MYMxsYSTnoVgiynjM+AIMQ#,#server.ccl.net> X-Original-From: James Womack Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Sat, 05 Feb 2011 17:05:45 +0000 MIME-Version: 1.0 Sent to CCL by: James Womack [james.c.womack||gmail.com] I can't offer any suggestions on how to fix the problem but I can tell you that it's not a problem with Ubuntu generally. I'm running version 2010.1 (compiled from source) without problem on Ubuntu 10.04 32 bit. As someone else said, it's worth going to the Molpro developers/mailing list directly with this problem. Hope you fix it soon, James On 04/02/11 07:03, Sidney Ramos Santana santanasidney:_:yahoo.com.br wrote: > Sent to CCL by: "Sidney Ramos Santana" [santanasidney||yahoo.com.br] > Dear CCL Users, > > Please could anyone help me? > > I am trying to execute the Molpro 2009 in a computer with > > Ubuntu 10.04 64 bits (Kernel Version: 2.6.32-28 SMP, and > > libc6 Version: 2.11.1-0ubuntu7.8). > > But the program have been stopped > > and typed the following error: > > /opt/molpro/bin/molprop_2009_1_Linux_x86_64_i8.exe, len=50 > cf3cl_8.inp, len=11 > -master, len=7 > ubuntu, len=6 > 39720, len=5 > 1, len=1 > 1, len=1 > 0, len=1 > 0, len=1 > molprop_2009_1_Linux_x86_64_i8.exe: relocation error: /lib/libnss_files.so.2: > symbol __r awmemchr, version GLIBC_2.2.5 not defined in file libc.so.6 with > link time reference > tmp = /home/sidney/pdir//opt/molpro/bin/molprop_2009_1_Linux_x86_64_i8.exe.p > Creating: host=ubuntu, user=elizete, > file=/opt/molpro/bin/molprop_2009_1_Linux_x86_64_i8.exe, port=39720 > 1: interrupt(1) > > Is this a Ubuntu version problem ? > > Please could anyone tell me what is wrong and how can I fix that ? > > Thanks for any help. > > Best Regards, > > Sidney R. Santana> >