[gmx-users] writing trajectory with water molecules within a distance from protein
tevang3 at gmail.com
Tue May 10 12:38:19 CEST 2011
A work around will be available in the future as a plugin for VMD.
For your reference read these threads:
On 10 May 2011 03:12, Roland Schulz <roland at utk.edu> wrote:
> 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
> What is possible is writing a small script around trjconv to produce one
> gro/trr file per frame with only those atoms.
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