[gmx-users] writing trajectory with water molecules within a distance from protein
mariagoranovic at gmail.com
Tue May 10 09:17:00 CEST 2011
So, one can probably do this using a simple script?
for each frame
make index file of water molecules within 0.5 nm using g_select
extract frame based on above selection
The only problem with the above would be that the number of water molecules
selected might change with each frame. Is there a way of choosing the
closest, say, 1000 water molecules using g_select
On Tue, May 10, 2011 at 12:28 AM, 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.
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Technical University of Denmark
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