[gmx-users] boundwaters

[shahid nayeem]

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.
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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