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

[maria goranovic]

An update on this. I got the following to work:

1. use a vmd script closest.tcl (available on the vmd pages) to select
closest N waters, and write a pdb file for each frame.

2. however, the above pdb files have different residue numbers for the water
molecules for each frame because it is not the same N waters each frame. So
use editconf to convert the pdbs to gros  with the -resnr 1 option

3. concatenate the frames using trjcat ( -cat option)

4. make the correct time spacing using trjconv. (-timestep)

The method is kinda tedious, but the final result is a trajectory of the
protein with closest N-waters updated every step. Good enough for my
analysis.

On Tue, May 10, 2011 at 12:38 PM, Thomas Evangelidis <tevang3 at gmail.com>wrote:

> 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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-- 
Maria G.
Technical University of Denmark
Copenhagen
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