[gmx-users] Freeze group atoms changing position
chris.neale at mail.utoronto.ca
Wed Oct 31 20:22:22 CET 2012
No need to rename... just make an .ndx group.
-- original message --
As I understand it, position restraints for an atom are set in the topology
file and applied to that atom in each of that species. In order to restrain
some but not all of the water I'd have to copy the topology of my water
model and add the restraints, then rename (and group together) the atoms I
want to freeze so that they're identified with the appropriate topology
file. Does this sound like it would work? Is there some other way that you
might do it?
On Fri, Oct 26, 2012 at 5:18 PM, Alex Marshall <amarsh59 at uwo.ca> wrote:
> Justin: I'll try using position restraints instead of freezing the water
> in the tube. Thanks for the tip.
> Bogdan: I don't think I'm using constraints other than freeze groups. I
> wasn't using energy group exclusions though. I tried running the simulation
> from the same initial configuration with newly-defined energy groups
> CNT_GRA_WAL_IN and OUT, the first for the frozen atoms and the second for
> the free atoms. The list of exclusions reads:
> energygrp_excl = CNT_GRA_WAL_IN CNT_GRA_WAL_IN
> Long story short, I'm roughly 15 ns into the simulation and the same two
> waters have jumped. I'll check the manual again though. Thanks.
> On Thu, Oct 25, 2012 at 10:43 AM, Bogdan Costescu <bcostescu at gmail.com>wrote:
>> On Thu, Oct 25, 2012 at 3:59 PM, Alex Marshall <amarsh59 at uwo.ca> wrote:
>> > Thanks Justin. I identified the offending waters using vmd (adding 1 to
>> > resID and atom number since vmd starts counting at 0) and checked
>> > confout.gro to make sure the coordinates matched up. I only have one
>> > for all frozen atoms in the system, and these guys are definitely in it.
>> Are you using some kind of constraints ? Are you using energy group
>> exclusions to avoid interactions between frozen atoms ? If you search
>> the manual for "frozen" you'll find some warnings and recommendations.
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> Alex Marshall
> M.Sc. Candidate
> Department of Applied Mathematics
> The University of Western Ontario
Department of Applied Mathematics
The University of Western Ontario
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