[gmx-users] Freeze group atoms changing position

[Justin Lemkul]

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.

-Justin

> 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?
>>
>> Thanks
>>
>> 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
>>>> group
>>>>> 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.
>>>>
>>>> Cheers,
>>>> Bogdan
>>>> --
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>>>
>>>
>>>
>>> --
>>> Alex Marshall
>>> M.Sc. Candidate
>>> Department of Applied Mathematics
>>> The University of Western Ontario
>>>
>>>
>>
>>
>> --
>> Alex Marshall
>> M.Sc.
>> Department of Applied Mathematics
>> The University of Western Ontario
>> --
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>
>
>

-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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