[gmx-users] Freeze group atoms changing position
jalemkul at vt.edu
Wed Oct 31 20:57:24 CET 2012
On 10/31/12 3:55 PM, Alex Marshall wrote:
> Chris, is that for freeze groups or position restraints?
I will assume Chris was referring to the restraint method - you need an index
file for creating the position restraint .itp file using genrestr. It will save
you a ton of time over doing it manually.
> On Wed, Oct 31, 2012 at 3:22 PM, Christopher Neale <
> chris.neale at mail.utoronto.ca> wrote:
>> 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
>>> 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
>>>> On Thu, Oct 25, 2012 at 3:59 PM, Alex Marshall <amarsh59 at uwo.ca>
>>>>> Thanks Justin. I identified the offending waters using vmd (adding 1
>>>>> 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
>>>> 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
>> Alex Marshall
>> Department of Applied Mathematics
>> The University of Western Ontario
>> gmx-users mailing list gmx-users at gromacs.org
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Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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