[gmx-users] how to select 'P' atom for g_msd

Justin A. Lemkul jalemkul at vt.edu
Thu Jun 26 18:07:04 CEST 2008

sudheer babu wrote:
> Hi Users,
>              I want to calculate lateral diffusion coefficent of popc 
> bilayer by using g_msd , the information I understood from one journal 
> (http://dx.doi.org/10.1063/1.2393240) is that  P atom select  and feed 
> to g_msd command . I have to take only single P atom or all Patoms of 
> POPC biliayer ? and how can i select by using make_ndx? Could you 
> please tell me

A single P atom will give you the diffusion coefficient for a single 
lipid, which I assume is not what you're after.

You can type 'h' at the make_ndx prompt to see some examples of how to 
create groups.


> Thanks in advance.
> ------------------------------------------------------------------------
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php


Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list