[gmx-users] Restraining water

[Oliver Grant]

I would use grep and cut to take the atom numbers of the residues I want to
restrain and direct them into an index file with [res_sol] at the top. Then
use genrestr to generate restraints for these atoms using the -n option.
Then conditionally include this restraint file (.itp file) in my topology
when you use -DPOSRES_res_sol (or whatever just make it match what's in the
top file) in your mdp file.

Thats how I would put position restraints on parts of my system. I think
different constraints are answered here too :)
Good luck,
Oliver



On 2 December 2010 08:21, David Rodríguez <david.rguez.diaz at gmail.com>wrote:

> 2010/12/2 Mark Abraham <Mark.Abraham at anu.edu.au>
>
> On 2/12/2010 12:51 PM, Guido Polles wrote:
>>
>>> Hi,
>>> I know it looks a little bit strange, but i was trying to restrain
>>> just some water in my system.
>>> Now, if i put something like
>>> [ position_restraints ]
>>> ;  i funct       fcx        fcy        fcz
>>>    1    1       1000       1000       1000
>>> I put restraints on all the molecules.
>>>
>>
>> Yes, that directive will pertain to all the molecules that have that [
>> moleculetype ]. I'm not sure if you only want position restraints on some of
>> your water molecules.
>>
>>
>>  I thought about a turnaround,  just making a second water molecule
>>> type, but now complains about using more than one settle type.
>>> Is there any other way to do it?
>>>
>>
> Guido,
> You may find this thread useful:
> http://lists.gromacs.org/pipermail/gmx-users/2010-September/054087.html
>
>
>> And if I follow the "Suggestion: change the least use settle
>>> constraints into 3 normal constraints" I have to worry about some kind
>>> of huge loss in performance?
>>>
>>
>> I would expect the non-settle waters to use the solvent-optimized loops in
>> the normal way, so there should be no difference in execution time between
>> the unrestrained all-settle simulation and the partly-restrained
>> party-settled simulation. Obviously, this is straightforward to test.
>>
>> Mark
>>
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>
>
>
> --
> David Rodríguez Díaz, PhD Student
> Fundación Pública Galega de Medicina Xenómica (SERGAS)
> Web page: http://webspersoais.usc.es/persoais/david.rodriguez.diaz
>
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