[gmx-users] Restraining water

[David Rodríguez]

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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