From owner-chemistry@ccl.net Sun Aug 5 05:55:01 2007 From: "=?ISO-8859-1?Q?Sina_T=FCreli?= sinatureli-,-gmail.com" To: CCL Subject: CCL: Freezing Atoms Message-Id: <-34882-070805043547-2211-Y2TZGRDc95QrEoMPRGrWgA|-|server.ccl.net> X-Original-From: "=?ISO-8859-1?Q?Sina_T=FCreli?=" Content-Type: multipart/alternative; boundary="----=_Part_51515_26113119.1186302912688" Date: Sun, 5 Aug 2007 11:35:12 +0300 MIME-Version: 1.0 Sent to CCL by: "=?ISO-8859-1?Q?Sina_T=FCreli?=" [sinatureli%x%gmail.com] ------=_Part_51515_26113119.1186302912688 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline I have checked that frozen atoms in the calculation window :) It seems to sometimes ignore that and sometimes not. I have made a succesful SE calculation with the atoms frozen. I am not yet sure what makes the difference On 8/5/07, Dave Hose anthrax_brothers_+_hotmail.com wrote: > > > Sent to CCL by: "Dave Hose" [anthrax_brothers~!~hotmail.com] > Have you checked the "Subject To: Frozen Atoms" box in the calculations > set up dialogue box? You > may have marked the atoms as frozen in the GUI, but the calculation will > ignore these frozen atoms > unless told otherwise. > > Regards, > > Dave. > > >Hello, > > > >I have a problem with freezing atoms in spartan. When I freeze them and > perform > >molecular mechanics calculations, the frozen atoms move all around. I am > sure > >that none of the atoms overlap with each other or are in extreme > proximities... > >(Someone told me that, it could have happened due to unacceptable > placement of > >atoms). I am afraid that it might do the same thing with SE calculations > too so > >before moving to SE calculations I want to fix this problem and > understand why > >it happens. I hope you can help me with this matter... Also is there any > other > >program where we can freeze atoms and do SE calculations? Thanks> > > > ------=_Part_51515_26113119.1186302912688 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline I have checked that frozen atoms in the calculation window :)
It seems to sometimes ignore that and sometimes not.  I  have made a succesful SE calculation with the atoms frozen. I am not yet sure what makes the difference

On 8/5/07, Dave Hose anthrax_brothers_+_hotmail.com <owner-chemistry..ccl.net> wrote:

Sent to CCL by: "Dave  Hose" [anthrax_brothers~!~hotmail.com]
Have you checked the "Subject To: Frozen Atoms" box in the calculations set up dialogue box?  You
may have marked the atoms as frozen in the GUI, but the calculation will ignore these frozen atoms
unless told otherwise.

Regards,

Dave.

>Hello,
>
>I have a problem with freezing atoms in spartan. When I freeze them and perform
>molecular mechanics calculations, the frozen atoms move all around. I am sure
>that none of the atoms overlap with each other or are in extreme proximities...
>(Someone told me that, it could have happened due to unacceptable placement of
>atoms). I am afraid that it might do the same thing with SE calculations too so
>before moving to SE calculations I want to fix this problem and understand why
>it happens. I hope you can help me with this matter... Also is there any other
>program where we can freeze atoms and do SE calculations? Thanks



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