[gmx-users] boundwaters

[Justin Lemkul]

On 1/28/13 10:53 AM, shahid nayeem wrote:
> Hi Justin
>   If I use the boundwaters.ndx to write another .ndx file using 1 & 2 &
> 3 & 4 and so on over all snapshots then also I should get the common
> water molecules in these snapshots. Am I right.

Presumably.  Probably faster to try it and see rather than spend time writing 
and email and waiting for a reply :)

-Justin

> Shahid
>
> On Mon, Jan 28, 2013 at 9:03 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>> On 1/28/13 10:02 AM, shahid nayeem wrote:
>>>
>>> Dear Users
>>> I am interested in knowing only the  water molecules which remains
>>> bounded to the protein during MD. Using g_select I can make a
>>> boundwater.ndx file which gives water molecules within a specified
>>> distance from the protein but it gives different water molecule from
>>> each snapshot. Now I want onle those water which is common in all
>>> frames. How to proceed from here and is there any other way to do
>>> this. Please help.
>>
>>
>> You should be able to write a simple script that runs through each group,
>> stores the atom numbers, and then checks which ones are common to all
>> frames.
>>
>> -Justin
>>
>> --
>> ========================================
>>
>> Justin A. Lemkul, Ph.D.
>> Research Scientist
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
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-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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