[gmx-developers] Pull to COM of molecules

[Carsten Kutzner]

On Apr 16, 2009, at 4:03 PM, chris.neale at utoronto.ca wrote:

> I can't comment from a code level, but I have been doing this  
> recently in my simulations. It was key for me to set pull_pbcatom0  
> to be an atom that is generally in the center of the reference  
> group. Then either 1) the box must be big enough that the other  
> atoms in that group are always placed in the same cluster (not  
> necessarily the same unit cell), or 2) the run must be completed in  
> segments and some script should exist to rationally choose an  
> optimal central pull_pbcatom0 to start the next short mdrun segment.
>
> Both of these are a little frustrating and myself and one other user  
> are currently getting some strange results in combination with the  
> free energy code, even with large boxes, but it certainly appears to  
> be working as expected.
>
> I have an item on the wiki wish list that outlines how the situation  
> could be dramatically improved here, and I have been in contact with  
> a programmer to get this modification made, although that will take  
> some months.

There is some code in edsam.c (ed_get_shifts) that puts an arbitrary  
group of atoms together each
time step by keeping track of shift changes. This way the group stays  
intact and each atom trajectory
is continuous throughout the run, which was needed for ED. I think  
this could also be used for large
pull groups.

Carsten

>
> Chris.
>
> Quoting David van der Spoel <spoel at xray.bmc.uu.se>:
>
>> Hi,
>>
>> is it possible to pull somehting to the center of mass of a group of
>> molecules? My guess (and preliminary experience) seems to say that  
>> this
>> is not possible due to the periodic boundary conditions. Does the
>> virtual site construction for center of mass solve this?
>>
>> -- 
>> David van der Spoel, Ph.D., Professor of Biology
>> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala  
>> University.
>> Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax:  
>> +4618511755.
>> spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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>
>
>
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--
Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics
Am Fassberg 11, 37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302
http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne