[gmx-users] Making an index file for specific solvent molecules

[Justin Lemkul]

On 1/20/20 11:31 AM, Aharon Gomez wrote:
> Hi everyone,
>
> I'm working on gas like molecules diffusion in protein. I have an equilibrated system and now I want
> to replace solvent molecules with some other molecule, like O2, but i want to select just the water molecules
> that are placed over some distance to my protein.
> Is there any built in tool in gromacs to make an index file of these solvent molecules or any other way to do it?

You can use gmx select to select atoms/molecules based on distance 
criteria. See syntax examples with "gmx help selections"

-Justin

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Justin A. Lemkul, Ph.D.
Assistant Professor
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Virginia Tech Department of Biochemistry
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jalemkul at vt.edu | (540) 231-3129
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