From owner-chemistry@ccl.net Thu May 21 00:07:00 2015
From: "sulgi lim sulgi8941(_)gmail.com" <owner-chemistry::server.ccl.net>
To: CCL
Subject: CCL: force field of amber14
Message-Id: <-51390-150520230157-12985-uF/iNo5GcWLCce+QB+dQNQ::server.ccl.net>
X-Original-From: sulgi lim <sulgi8941:gmail.com>
Content-Type: multipart/alternative; boundary=089e0158cba0e57e9c05168ec356
Date: Thu, 21 May 2015 12:01:51 +0900
MIME-Version: 1.0


Sent to CCL by: sulgi lim [sulgi8941.:.gmail.com]
--089e0158cba0e57e9c05168ec356
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: quoted-printable

To whom it may concern,



This is Sulgi, a M.S. candidate and user of amber14.



I=E2=80=99m writing to enquire about force field of amber14.

When I tried to making new topology with my system, I read amber14
tutorials and did leap process using below command.



Tleap =E2=80=93s =E2=80=93f $AMBERHOME/dat/leap/cmd/leaprc.ff14SB

Source leaprc.gaff

Loadamberparams frcmod.ff99SB14



However, few days later, I found that force field reads parm10.dat.

When I used amber11, parm99.dat was in log file formed by leap.

Ph. D in my lab. let me know the right commands for ff99SB force field, but
I am wondering if I can use my system based on parm10.dat.

Is it a big difference or serious problem between parm10.dat and
parm99.dat??

What is differences between the two?

Could you please explain me?

(If I send mail to wrong address, then please let me know.)



Thank you for your consideration.



Sincerely,

Sulgi

--089e0158cba0e57e9c05168ec356
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Content-Transfer-Encoding: quoted-printable

<div dir=3D"ltr"><p style=3D"margin:0px;padding:0px;color:rgb(51,51,51);fon=
t-family:=EB=8F=8B=EC=9B=80;font-size:13.3333330154419px;line-height:20px">=
<span style=3D"font-size:10pt;line-height:1.5">To whom it may concern,</spa=
n></p><p style=3D"margin:0px;padding:0px;color:rgb(51,51,51);font-family:=
=EB=8F=8B=EC=9B=80;font-size:13.3333330154419px;line-height:20px">=C2=A0</p=
><p style=3D"margin:0px;padding:0px;color:rgb(51,51,51);font-family:=EB=8F=
=8B=EC=9B=80;font-size:13.3333330154419px;line-height:20px">This is Sulgi, =
a M.S. candidate and user of amber14.</p><p style=3D"margin:0px;padding:0px=
;color:rgb(51,51,51);font-family:=EB=8F=8B=EC=9B=80;font-size:13.3333330154=
419px;line-height:20px">=C2=A0</p><p style=3D"margin:0px;padding:0px;color:=
rgb(51,51,51);font-family:=EB=8F=8B=EC=9B=80;font-size:13.3333330154419px;l=
ine-height:20px">I=E2=80=99m writing to enquire about force field of amber1=
4.</p><p style=3D"margin:0px;padding:0px;color:rgb(51,51,51);font-family:=
=EB=8F=8B=EC=9B=80;font-size:13.3333330154419px;line-height:20px">When I tr=
ied to making new topology with my system, I read amber14 tutorials and did=
 leap process using below command.</p><p style=3D"margin:0px;padding:0px;co=
lor:rgb(51,51,51);font-family:=EB=8F=8B=EC=9B=80;font-size:13.3333330154419=
px;line-height:20px">=C2=A0</p><p style=3D"margin:0px;padding:0px;color:rgb=
(51,51,51);font-family:=EB=8F=8B=EC=9B=80;font-size:13.3333330154419px;line=
-height:20px">Tleap =E2=80=93s =E2=80=93f $AMBERHOME/dat/leap/cmd/leaprc.ff=
14SB</p><p style=3D"margin:0px;padding:0px;color:rgb(51,51,51);font-family:=
=EB=8F=8B=EC=9B=80;font-size:13.3333330154419px;line-height:20px">Source le=
aprc.gaff</p><p style=3D"margin:0px;padding:0px;color:rgb(51,51,51);font-fa=
mily:=EB=8F=8B=EC=9B=80;font-size:13.3333330154419px;line-height:20px">Load=
amberparams frcmod.ff99SB14</p><p style=3D"margin:0px;padding:0px;color:rgb=
(51,51,51);font-family:=EB=8F=8B=EC=9B=80;font-size:13.3333330154419px;line=
-height:20px">=C2=A0</p><p style=3D"margin:0px;padding:0px;color:rgb(51,51,=
51);font-family:=EB=8F=8B=EC=9B=80;font-size:13.3333330154419px;line-height=
:20px">However, few days later, I found that force field reads parm10.dat.<=
/p><p style=3D"margin:0px;padding:0px;color:rgb(51,51,51);font-family:=EB=
=8F=8B=EC=9B=80;font-size:13.3333330154419px;line-height:20px">When I used =
amber11, parm99.dat was in log file formed by leap.</p><p style=3D"margin:0=
px;padding:0px;color:rgb(51,51,51);font-family:=EB=8F=8B=EC=9B=80;font-size=
:13.3333330154419px;line-height:20px">Ph. D in my lab. let me know the righ=
t commands for ff99SB force field, but I am wondering if I can use my syste=
m based on parm10.dat.</p><p style=3D"margin:0px;padding:0px;color:rgb(51,5=
1,51);font-family:=EB=8F=8B=EC=9B=80;font-size:13.3333330154419px;line-heig=
ht:20px">Is it a big difference or serious problem between parm10.dat and p=
arm99.dat??</p><p style=3D"margin:0px;padding:0px;color:rgb(51,51,51);font-=
family:=EB=8F=8B=EC=9B=80;font-size:13.3333330154419px;line-height:20px">Wh=
at is differences between the two?</p><p style=3D"margin:0px;padding:0px;co=
lor:rgb(51,51,51);font-family:=EB=8F=8B=EC=9B=80;font-size:13.3333330154419=
px;line-height:20px">Could you please explain me?</p><p style=3D"margin:0px=
;padding:0px;color:rgb(51,51,51);font-family:=EB=8F=8B=EC=9B=80;font-size:1=
3.3333330154419px;line-height:20px">(If I send mail to wrong address, then =
please let me know.)</p><p style=3D"margin:0px;padding:0px;color:rgb(51,51,=
51);font-family:=EB=8F=8B=EC=9B=80;font-size:13.3333330154419px;line-height=
:20px">=C2=A0</p><p style=3D"margin:0px;padding:0px;color:rgb(51,51,51);fon=
t-family:=EB=8F=8B=EC=9B=80;font-size:13.3333330154419px;line-height:20px">=
Thank you for your consideration.</p><p style=3D"margin:0px;padding:0px;col=
or:rgb(51,51,51);font-family:=EB=8F=8B=EC=9B=80;font-size:13.3333330154419p=
x;line-height:20px">=C2=A0</p><p style=3D"margin:0px;padding:0px;color:rgb(=
51,51,51);font-family:=EB=8F=8B=EC=9B=80;font-size:13.3333330154419px;line-=
height:20px">Sincerely,</p><p style=3D"margin:0px;padding:0px;color:rgb(51,=
51,51);font-family:=EB=8F=8B=EC=9B=80;font-size:13.3333330154419px;line-hei=
ght:20px">Sulgi</p></div>

--089e0158cba0e57e9c05168ec356--


From owner-chemistry@ccl.net Thu May 21 02:24:01 2015
From: "Kshatresh Dutta Dubey kshatresh**gmail.com" <owner-chemistry||server.ccl.net>
To: CCL
Subject: CCL: force field of amber14
Message-Id: <-51391-150521022252-13177-JDVd0JHCfojLP2/l1hGGVA||server.ccl.net>
X-Original-From: Kshatresh Dutta Dubey <kshatresh^^^gmail.com>
Content-Type: multipart/alternative; boundary=047d7b86cae067ba1205169192ba
Date: Thu, 21 May 2015 09:22:45 +0300
MIME-Version: 1.0


Sent to CCL by: Kshatresh Dutta Dubey [kshatresh : gmail.com]
--047d7b86cae067ba1205169192ba
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: quoted-printable

Hi Sulgi,

I wonder why are you using ff99SB when you have Amber14. The recent and
updated amber forcefield is ff14SB which is always recommended.
Furthermore, you didn't mention the error when sourced leaprc.ff14SB. What
was the problem in sourcing  leaprc.ff14SB? In addition, there is no need
to separately load frcmod.ff99SB, as it loads by default when you source
leaprc.ff14SB.

parm10.dat is updated parameters over parm99.dat, and always updated
parameters have merits over downgraded parameters. Its quite natural that
leap.log show you parm99.dat if you use amber 11 as it is three steps older
version of  Amber (I will say quite old). Therefore you must use parm10.dat
(ff14SB) which is new and updated parameters.

The best place to ask amber related question, is :  amber#,#ambermd.org

Regards
Kshatresh


On Thu, May 21, 2015 at 6:01 AM, sulgi lim sulgi8941(_)gmail.com <
owner-chemistry#,#ccl.net> wrote:

> To whom it may concern,
>
>
>
> This is Sulgi, a M.S. candidate and user of amber14.
>
>
>
> I=E2=80=99m writing to enquire about force field of amber14.
>
> When I tried to making new topology with my system, I read amber14
> tutorials and did leap process using below command.
>
>
>
> Tleap =E2=80=93s =E2=80=93f $AMBERHOME/dat/leap/cmd/leaprc.ff14SB
>
> Source leaprc.gaff
>
> Loadamberparams frcmod.ff99SB14
>
>
>
> However, few days later, I found that force field reads parm10.dat.
>
> When I used amber11, parm99.dat was in log file formed by leap.
>
> Ph. D in my lab. let me know the right commands for ff99SB force field,
> but I am wondering if I can use my system based on parm10.dat.
>
> Is it a big difference or serious problem between parm10.dat and
> parm99.dat??
>
> What is differences between the two?
>
> Could you please explain me?
>
> (If I send mail to wrong address, then please let me know.)
>
>
>
> Thank you for your consideration.
>
>
>
> Sincerely,
>
> Sulgi
>



--=20
With best regards
***************************************************************************=
*********************
Kshatresh Dutta Dubey
Post Doctoral Researcher,
Lise Meitner Center for Computational Quantum Chemistry
Hebrew University of Jerusalem Israel
Jerusalem, Israel

--047d7b86cae067ba1205169192ba
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<div dir=3D"ltr">Hi Sulgi,<div><br></div><div>I wonder why are you using ff=
99SB when you have Amber14. The recent and updated amber forcefield is ff14=
SB which is always recommended. Furthermore, you didn&#39;t mention the err=
or when sourced leaprc.ff14SB. What was the problem in sourcing =C2=A0leapr=
c.ff14SB? In addition, there is no need to separately load frcmod.ff99SB, a=
s it loads by default when you source leaprc.ff14SB.</div><div><br></div><d=
iv>parm10.dat is updated parameters over parm99.dat, and always updated par=
ameters have merits over downgraded parameters. Its quite natural that leap=
.log show you parm99.dat if you use amber 11 as it is three steps older ver=
sion of =C2=A0Amber (I will say quite old). Therefore you must use parm10.d=
at (ff14SB) which is new and updated parameters.=C2=A0</div><div><br></div>=
<div>The best place to ask amber related question, is : =C2=A0<a href=3D"ma=
ilto:amber#,#ambermd.org">amber#,#ambermd.org</a>=C2=A0</div><div><br></div><di=
v>Regards</div><div>Kshatresh</div><div><br></div></div><div class=3D"gmail=
_extra"><br><div class=3D"gmail_quote">On Thu, May 21, 2015 at 6:01 AM, sul=
gi lim sulgi8941(_)<a href=3D"http://gmail.com">gmail.com</a> <span dir=3D"=
ltr">&lt;<a href=3D"mailto:owner-chemistry#,#ccl.net" target=3D"_blank">owner=
-chemistry#,#ccl.net</a>&gt;</span> wrote:<br><blockquote class=3D"gmail_quot=
e" style=3D"margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">=
<div dir=3D"ltr"><p style=3D"margin:0px;padding:0px;color:rgb(51,51,51);fon=
t-family:=EB=8F=8B=EC=9B=80;font-size:13.3333330154419px;line-height:20px">=
<span style=3D"font-size:10pt;line-height:1.5">To whom it may concern,</spa=
n></p><p style=3D"margin:0px;padding:0px;color:rgb(51,51,51);font-family:=
=EB=8F=8B=EC=9B=80;font-size:13.3333330154419px;line-height:20px">=C2=A0</p=
><p style=3D"margin:0px;padding:0px;color:rgb(51,51,51);font-family:=EB=8F=
=8B=EC=9B=80;font-size:13.3333330154419px;line-height:20px">This is Sulgi, =
a M.S. candidate and user of amber14.</p><p style=3D"margin:0px;padding:0px=
;color:rgb(51,51,51);font-family:=EB=8F=8B=EC=9B=80;font-size:13.3333330154=
419px;line-height:20px">=C2=A0</p><p style=3D"margin:0px;padding:0px;color:=
rgb(51,51,51);font-family:=EB=8F=8B=EC=9B=80;font-size:13.3333330154419px;l=
ine-height:20px">I=E2=80=99m writing to enquire about force field of amber1=
4.</p><p style=3D"margin:0px;padding:0px;color:rgb(51,51,51);font-family:=
=EB=8F=8B=EC=9B=80;font-size:13.3333330154419px;line-height:20px">When I tr=
ied to making new topology with my system, I read amber14 tutorials and did=
 leap process using below command.</p><p style=3D"margin:0px;padding:0px;co=
lor:rgb(51,51,51);font-family:=EB=8F=8B=EC=9B=80;font-size:13.3333330154419=
px;line-height:20px">=C2=A0</p><p style=3D"margin:0px;padding:0px;color:rgb=
(51,51,51);font-family:=EB=8F=8B=EC=9B=80;font-size:13.3333330154419px;line=
-height:20px">Tleap =E2=80=93s =E2=80=93f $AMBERHOME/dat/leap/cmd/leaprc.ff=
14SB</p><p style=3D"margin:0px;padding:0px;color:rgb(51,51,51);font-family:=
=EB=8F=8B=EC=9B=80;font-size:13.3333330154419px;line-height:20px">Source le=
aprc.gaff</p><p style=3D"margin:0px;padding:0px;color:rgb(51,51,51);font-fa=
mily:=EB=8F=8B=EC=9B=80;font-size:13.3333330154419px;line-height:20px">Load=
amberparams frcmod.ff99SB14</p><p style=3D"margin:0px;padding:0px;color:rgb=
(51,51,51);font-family:=EB=8F=8B=EC=9B=80;font-size:13.3333330154419px;line=
-height:20px">=C2=A0</p><p style=3D"margin:0px;padding:0px;color:rgb(51,51,=
51);font-family:=EB=8F=8B=EC=9B=80;font-size:13.3333330154419px;line-height=
:20px">However, few days later, I found that force field reads parm10.dat.<=
/p><p style=3D"margin:0px;padding:0px;color:rgb(51,51,51);font-family:=EB=
=8F=8B=EC=9B=80;font-size:13.3333330154419px;line-height:20px">When I used =
amber11, parm99.dat was in log file formed by leap.</p><p style=3D"margin:0=
px;padding:0px;color:rgb(51,51,51);font-family:=EB=8F=8B=EC=9B=80;font-size=
:13.3333330154419px;line-height:20px">Ph. D in my lab. let me know the righ=
t commands for ff99SB force field, but I am wondering if I can use my syste=
m based on parm10.dat.</p><p style=3D"margin:0px;padding:0px;color:rgb(51,5=
1,51);font-family:=EB=8F=8B=EC=9B=80;font-size:13.3333330154419px;line-heig=
ht:20px">Is it a big difference or serious problem between parm10.dat and p=
arm99.dat??</p><p style=3D"margin:0px;padding:0px;color:rgb(51,51,51);font-=
family:=EB=8F=8B=EC=9B=80;font-size:13.3333330154419px;line-height:20px">Wh=
at is differences between the two?</p><p style=3D"margin:0px;padding:0px;co=
lor:rgb(51,51,51);font-family:=EB=8F=8B=EC=9B=80;font-size:13.3333330154419=
px;line-height:20px">Could you please explain me?</p><p style=3D"margin:0px=
;padding:0px;color:rgb(51,51,51);font-family:=EB=8F=8B=EC=9B=80;font-size:1=
3.3333330154419px;line-height:20px">(If I send mail to wrong address, then =
please let me know.)</p><p style=3D"margin:0px;padding:0px;color:rgb(51,51,=
51);font-family:=EB=8F=8B=EC=9B=80;font-size:13.3333330154419px;line-height=
:20px">=C2=A0</p><p style=3D"margin:0px;padding:0px;color:rgb(51,51,51);fon=
t-family:=EB=8F=8B=EC=9B=80;font-size:13.3333330154419px;line-height:20px">=
Thank you for your consideration.</p><p style=3D"margin:0px;padding:0px;col=
or:rgb(51,51,51);font-family:=EB=8F=8B=EC=9B=80;font-size:13.3333330154419p=
x;line-height:20px">=C2=A0</p><p style=3D"margin:0px;padding:0px;color:rgb(=
51,51,51);font-family:=EB=8F=8B=EC=9B=80;font-size:13.3333330154419px;line-=
height:20px">Sincerely,</p><p style=3D"margin:0px;padding:0px;color:rgb(51,=
51,51);font-family:=EB=8F=8B=EC=9B=80;font-size:13.3333330154419px;line-hei=
ght:20px">Sulgi</p></div>
</blockquote></div><br><br clear=3D"all"><div><br></div>-- <br><div class=
=3D"gmail_signature"><div dir=3D"ltr"><div><div dir=3D"ltr"><div>With best =
regards</div><div>*********************************************************=
***************************************<br>Kshatresh Dutta Dubey</div><div>=
Post Doctoral Researcher,<br></div><div>Lise Meitner Center for Computation=
al Quantum Chemistry<br>Hebrew University of Jerusalem Israel<br></div><div=
>Jerusalem, Israel<br><br><br></div></div></div></div></div>
</div>

--047d7b86cae067ba1205169192ba--


From owner-chemistry@ccl.net Thu May 21 12:43:00 2015
From: "Derek Cashman derek.cashman_+_gmail.com" <owner-chemistry+*+server.ccl.net>
To: CCL
Subject: CCL: Workshop on Computational Biophysics (Berkeley, Aug 3-7, 2015)
Message-Id: <-51392-150521123434-19898-ywNsWi38gWhfYzfdBAXTvA+*+server.ccl.net>
X-Original-From: Derek Cashman <derek.cashman() gmail.com>
Content-Type: multipart/alternative; boundary="Apple-Mail=_15DD2938-5AF6-45E1-9FB9-08F94D82E560"
Date: Thu, 21 May 2015 11:34:20 -0500
Mime-Version: 1.0 (Mac OS X Mail 8.2 \(2070.6\))


Sent to CCL by: Derek Cashman [derek.cashman(~)gmail.com]

--Apple-Mail=_15DD2938-5AF6-45E1-9FB9-08F94D82E560
Content-Transfer-Encoding: quoted-printable
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	charset=utf-8

> On May 20, 2015, at 9:38 PM, Billy McCann thebillywayne:+:gmail.com =
<owner-chemistry-.-ccl.net> wrote:
>=20
> Sent to CCL by: Billy McCann [thebillywayne]~[gmail.com =
<http://gmail.com/>]
>> Are you sure a discrete graphics card is required?
>=20
> That they specify a "graphics card" and not a "graphical processing
> unit" indicates, to me, that this workshop requires a laptop with a
> *discrete* graphics card and not an integrated graphics solution.
> Also the specific brand mentioned, nVidia, supplies *solely* discrete
> graphics solutions in consumer grade laptops.
>=20
> Also, consider the advice given regarding the Mac platform:
> "Macintosh computers often come with sufficient graphics processing
> power, so no additional card is necessary."
>=20
> By inference, non-Macintosh computers  *will* need an additional card.
>=20
> Overall, reading the laptop requirements page leaves me somewhat
> confused. (".... up-to-date hardware, operating systems, and software
> versions
> .... Windows 2000, Max OS X 10.3 ... G4 ... Pentium 4 ..." ???)

http://www.ks.uiuc.edu/Training/Workshop/Berkeley2015/Requirements.html =
<http://www.ks.uiuc.edu/Training/Workshop/Berkeley2015/Requirements.html>

The system specs listed are very low =E2=80=94 in the Windows realm, =
they don=E2=80=99t even mention Windows 7 or 8 (although I am sure that =
those would probably be fine since they are successors to XP & Vista). =
They also mention a Pentium 4 processor with 512 MB RAM =E2=80=94 a =
processor that was common from 2000 to 2008. Most systems now are Core =
i5 or Core i7, and even low-end systems have at least 1 or 2 GB of RAM, =
so 512 MB RAM is a very low requirement.

In the Mac realm, the G4 processor (minimum requirement) is 10-15 years =
old, and predates the intel Macs. OS X 10.3 is also very low =E2=80=94 =
their up to 10.10 (Yosemite) now (having left the era of the =E2=80=9Cbig =
cats=E2=80=9D behind several versions ago). And even my iPhone has more =
RAM than the 512 MB minimum requirement they specify.

=46rom my own experience with molecular dynamics simulations, I do think =
that a discrete graphics card will be an advantage, however. And as a =
Mac user, I may disagree with the statement that, =E2=80=9CMacintosh =
computers often come with sufficient graphics processing power, so no =
additional card is necessary.=E2=80=9D In fact, the higher end MacBook =
Pros do come with quite powerful nVidia or AMD graphics boards (the new =
ones have intel graphics as well, which they use for light tasks such as =
word processing, and switching into the higher discrete graphics for =
gaming or graphics visualization as needed). I have had students working =
with the FoldIt protein folding game using low-end Macs without discrete =
graphics cards that have not been able to complete the introductory =
levels of the game, as their computer crashed for not enough power (but =
these students also had low amounts of RAM as well).

Intel-based graphics has also come a long way, too. And an intel-based =
graphics with sufficient system RAM (say at least 8-16 GB) should be =
able to perform at least comparatively to some of the earlier discrete =
graphics boards from several years ago (such as the nVidia Geforce =
Ti4600 mentioned). But if you have 4 or less GB of system RAM, you could =
have problems.

I think if you=E2=80=99re uncertain whether your system meets the =
minimum requirements, the best approach would be to contact the workshop =
organizers and send them your system specs and ask them directly what =
their recommendation is. After all, they should be familiar with =
everything that they are planning to conduct, and would be most =
knowledgeable in finding out where your system falls short.


Derek J. Cashman, Ph.D.
derek.cashman-.-gmail.com <mailto:derek.cashman-.-gmail.com>

"A drug is any substance which, when injected into a rat, produces a =
publishable, scientific paper."


--Apple-Mail=_15DD2938-5AF6-45E1-9FB9-08F94D82E560
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	charset=utf-8

<html><head><meta http-equiv=3D"Content-Type" content=3D"text/html =
charset=3Dutf-8"></head><body style=3D"word-wrap: break-word; =
-webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" =
class=3D""><div class=3D""><blockquote type=3D"cite" class=3D""><div =
class=3D"">On May 20, 2015, at 9:38 PM, Billy McCann thebillywayne:+:<a =
href=3D"http://gmail.com" class=3D"">gmail.com</a> &lt;<a =
href=3D"mailto:owner-chemistry-.-ccl.net" =
class=3D"">owner-chemistry-.-ccl.net</a>&gt; wrote:</div><br =
class=3D"Apple-interchange-newline"><div class=3D""><span class=3D"" =
style=3D"float: none; display: inline !important;">Sent to CCL by: Billy =
McCann [thebillywayne]~[</span><a href=3D"http://gmail.com/" =
class=3D"">gmail.com</a><span class=3D"" style=3D"float: none; display: =
inline !important;">]</span><br class=3D""><blockquote type=3D"cite" =
class=3D"">Are you sure a discrete graphics card is required?<br =
class=3D""></blockquote><br class=3D""><span class=3D"" style=3D"float: =
none; display: inline !important;">That they specify a "graphics card" =
and not a "graphical processing</span><br class=3D""><span class=3D"" =
style=3D"float: none; display: inline !important;">unit" indicates, to =
me, that this workshop requires a laptop with a</span><br class=3D""><span=
 class=3D"" style=3D"float: none; display: inline =
!important;">*discrete* graphics card and not an integrated graphics =
solution.</span><br class=3D""><span class=3D"" style=3D"float: none; =
display: inline !important;">Also the specific brand mentioned, nVidia, =
supplies *solely* discrete</span><br class=3D""><span class=3D"" =
style=3D"float: none; display: inline !important;">graphics solutions in =
consumer grade laptops.</span><br class=3D""><br class=3D""><span =
class=3D"" style=3D"float: none; display: inline !important;">Also, =
consider the advice given regarding the Mac platform:</span><br =
class=3D""><span class=3D"" style=3D"float: none; display: inline =
!important;">"Macintosh computers often come with sufficient graphics =
processing</span><br class=3D""><span class=3D"" style=3D"float: none; =
display: inline !important;">power, so no additional card is =
necessary."</span><br class=3D""><br class=3D""><span class=3D"" =
style=3D"float: none; display: inline !important;">By inference, =
non-Macintosh computers &nbsp;*will* need an additional card.</span><br =
class=3D""><br class=3D""><span class=3D"" style=3D"float: none; =
display: inline !important;">Overall, reading the laptop requirements =
page leaves me somewhat</span><br class=3D""><span class=3D"" =
style=3D"float: none; display: inline !important;">confused. (".... =
up-to-date hardware, operating systems, and software</span><br =
class=3D""><span class=3D"" style=3D"float: none; display: inline =
!important;">versions</span><br class=3D""><span class=3D"" =
style=3D"float: none; display: inline !important;">.... Windows 2000, =
Max OS X 10.3 ... G4 ... Pentium 4 ..." =
???)</span></div></blockquote><br class=3D""></div><div class=3D""><a =
href=3D"http://www.ks.uiuc.edu/Training/Workshop/Berkeley2015/Requirements=
.html" =
class=3D"">http://www.ks.uiuc.edu/Training/Workshop/Berkeley2015/Requireme=
nts.html</a></div><div class=3D""><br class=3D""></div><div class=3D"">The=
 system specs listed are very low =E2=80=94 in the Windows realm, they =
don=E2=80=99t even mention Windows 7 or 8 (although I am sure that those =
would probably be fine since they are successors to XP &amp; Vista). =
They also mention a Pentium 4 processor with 512 MB RAM =E2=80=94 a =
processor that was common from 2000 to 2008. Most systems now are Core =
i5 or Core i7, and even low-end systems have at least 1 or 2 GB of RAM, =
so 512 MB RAM is a very low requirement.</div><div class=3D""><br =
class=3D""></div><div class=3D"">In the Mac realm, the G4 processor =
(minimum requirement) is 10-15 years old, and predates the intel Macs. =
OS X 10.3 is also very low =E2=80=94 their up to 10.10 (Yosemite) now =
(having left the era of the =E2=80=9Cbig cats=E2=80=9D behind several =
versions ago). And even my iPhone has more RAM than the 512 MB minimum =
requirement they specify.</div><div class=3D""><br class=3D""></div><div =
class=3D"">=46rom my own experience with molecular dynamics simulations, =
I do think that a discrete graphics card will be an advantage, however. =
And as a Mac user, I may disagree with the statement that, =E2=80=9CMacint=
osh computers often come with sufficient graphics processing power, so =
no additional card is necessary.=E2=80=9D In fact, the higher end =
MacBook Pros do come with quite powerful nVidia or AMD graphics boards =
(the new ones have intel graphics as well, which they use for light =
tasks such as word processing, and switching into the higher discrete =
graphics for gaming or graphics visualization as needed). I have had =
students working with the FoldIt protein folding game using low-end Macs =
without discrete graphics cards that have not been able to complete the =
introductory levels of the game, as their computer crashed for not =
enough power (but these students also had low amounts of RAM as =
well).</div><div class=3D""><br class=3D""></div><div =
class=3D"">Intel-based graphics has also come a long way, too. And an =
intel-based graphics with sufficient system RAM (say at least 8-16 GB) =
should be able to perform at least comparatively to some of the earlier =
discrete graphics boards from several years ago (such as the nVidia =
Geforce Ti4600 mentioned). But if you have 4 or less GB of system RAM, =
you could have problems.</div><div class=3D""><br class=3D""></div><div =
class=3D"">I think if you=E2=80=99re uncertain whether your system meets =
the minimum requirements, the best approach would be to contact the =
workshop organizers and send them your system specs and ask them =
directly what their recommendation is. After all, they should be =
familiar with everything that they are planning to conduct, and would be =
most knowledgeable in finding out where your system falls =
short.</div><div class=3D""><br class=3D""></div><div class=3D""><br =
class=3D""></div><div class=3D"">
<div class=3D"">Derek J. Cashman, Ph.D.<br class=3D""><a =
href=3D"mailto:derek.cashman-.-gmail.com" =
class=3D"">derek.cashman-.-gmail.com</a><br class=3D""><br class=3D"">"A =
drug is any substance which, when injected into a rat, produces a =
publishable, scientific paper."</div>

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