[gmx-users] Freeze group atoms changing position

Alex Marshall amarsh59 at uwo.ca
Thu Nov 8 14:59:11 CET 2012 

Just as an update, I ran the simulation using position restraints with
force constants set to 10000 for each atom in the restrained waters, and
none jumped out of the nanotube. Thanks for the help!

On Thu, Nov 1, 2012 at 5:01 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 11/1/12 4:56 PM, Alex Marshall wrote:
>
>> I've created a position restraint file for the specific waters that I need
>> to immobilize, but I'm having a hard time getting grompp to apply it
>> successfully. No matter where I put #include "posre.itp" in my topology
>> file grompp returns fatal errors about the atomic indices being out of
>> bounds. Is it actually possible to only apply position restraints to some
>> molecules within a species and leave the rest alone?
>>
>>
> Yes, but you can't simply #include "spc.itp" and then call the position
> restraint file, for example.  You need a [moleculetype] for the entire
> block of water, since position restraints can only be applied per
> [moleculetype].
>
> -Justin
>
>  On Wed, Oct 31, 2012 at 3:57 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>>
>>> 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
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>>> http://www.bevanlab.biochem.****vt.edu/Pages/Personal/justin<http://vt.edu/Pages/Personal/justin>
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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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
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-- 
Alex Marshall
M.Sc.
Department of Applied Mathematics
The University of Western Ontario

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