[gmx-developers] Pull to COM of molecules

[hessb at mpip-mainz.mpg.de]

Hi,

The ED solution, stricktly speaking, only works for a single
molecule, because with multiple molecules one molecule in the cluster
could move away from the cluster and attach again displaced by nearly
a periodic distance. This will introduce nasty problems and artifacts.

I have implemented a proper solution which is already in 4.0 (hidden),
but we are still writing up the paper.
I can contact people off list (end of next week, we are currently
on holiday and are moving to Stockholm beginning of next week),
to explain how the method works.

Berk

> 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
>
>
>
>
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