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.
-Justin
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 [email protected]
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 [email protected].
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
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/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/mailing_lists/users.php
