[gmx-users] writing trajectory with water molecules within a distance from protein

[Roland Schulz]

On Mon, May 9, 2011 at 6:28 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

> On 10/05/2011 12:50 AM, maria goranovic wrote:
>
>> Dear experts
>>
>> I have a protein simulation in a water box. I now want to write a
>> trajectory containing only the protein, and water molecules within 5
>> Angstroms of the protein, with the water list being updated each time step.
>> How can one do this? Appreciate the help
>>
>
> g_select is useful for "dynamic" selections of this type. g_select -select
> "help" can give examples and such.
>
> I'd hope it's been designed so that then using trjconv to extract such
> selections works, but I can't think how, having not ever tried.
>
g_select writes out one index group per time frame. But trjconv can't use a
different index group for each frame. Thus it can't be used to write out a
trajectory with those atoms for each frame.  Part of the problem is that the
trajectory format doesn't support different number of atoms for different
frames.
What is possible is writing a small script around trjconv to produce one
gro/trr file per frame with only those atoms.

Roland


> Mark
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