[gmx-users] water handling

[Ken Rotondi]

Phuong/all,

Thanks, but perhaps I wasn't sufficiently clear as to my needs. Your 
method requires an "index.ndx" file containing the index of the atoms 
in my protein as well as the "N waters that are closest to the 
protein". However, I was effectively wondering how to generate this 
index, i.e. I do not know, a priori, what waters are close to the 
protein, I was hoping to map them somehow w/in GROMACS (e.g. 
retain/report solvent molecules XÅ from a protein atom) and use your 
method to then remove all the bulk water retaining only those close to 
the protein.

K


On Tuesday, March 9, 2004, at 11:40 AM, Nguyen Hoang Phuong wrote:

> On Tue, 9 Mar 2004, Ken Rotondi wrote:
>
>> Hello,
>>
>> I've run some trajectories in explicit solvent. I'd like to observe 
>> the
>> behavior of the water molecules in the first several layers of solvent
>> around the protein. Is there any way in the GROMACS package that I can
>> strip away the bulk water and look at snapshots of just the protein 
>> and
>> its associated waters? I've looked through trjconv but did not see a
>> solution to my need.
>>
>> As always, thanks in advance for any help,
>>
>> Ken
>>
>> K.S.Rotondi
>> Research Associate
>> The Gierasch Laboratory
>> The University of Massachusetts-Amherst
>
> you can use trjorder and trjconv for your need.
>
> trjorder -f xxx.trr -s xxx.tpr -o xxx_order.trr
>
> trjconv_d  -f xxx_order.trr -s xxx.tpr -n index.ndx -o yyy.gro
>
> where index.ndx is the index file containning the index of atoms of 
> your
> protein and N waters which are closest to the protein.
>
> Phuong
>
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K.S.Rotondi
Research Associate
The Gierasch Laboratory
The University of Massachusetts-Amherst