[gmx-users] large force on an atom

Justin A. Lemkul jalemkul at vt.edu
Tue Jul 21 15:55:16 CEST 2009

Samik Bhattacharya wrote:
> hi, i'm simulating a membrane protein in DPPC bilayer. here i'm using 
> inflategro perl script. just after the first run when i'm running grompp 
> to minimize it i have found a large force on a phenylalanin atom which 
> is well over 10^15   ^ Now what to do with this one?  I had a view of 
> that particular atom through pymol which is an Oxygen (CO). Right now 
> I’m a little anxious that if I keep this and go on it’ll affect the 
> future steps. Any suggestions regarding this will be very encouraging..

Well, is that atom clashing with something else in your system?  The only way I 
can think to get a force of 10^15 is substantial atomic overlap.


> Thank You
> Shamik
> ------------------------------------------------------------------------
> Yahoo! recommends that you upgrade to the new and safer Internet 
> Explorer 8 
> <http://in.rd.yahoo.com/tagline_ie8_1/*http://downloads.yahoo.com/in/internetexplorer/>. 
> ------------------------------------------------------------------------
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.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
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list