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 <[email protected]> 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
========================================
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the www
interface or send it to [email protected].
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
========================================
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
========================================
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
