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

[Thomas Evangelidis]

A work around will be available in the future as a plugin for VMD.

For your reference read these threads:

http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/14140.html

http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/13217.html


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
> 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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>>
>
>
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-- 

======================================================================

Thomas Evangelidis

PhD student

Biomedical Research Foundation, Academy of Athens

4 Soranou Ephessiou , 115 27 Athens, Greece

email: tevang at bioacademy.gr

          tevang3 at gmail.com


website: https://sites.google.com/site/thomasevangelidishomepage/
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