Rebeca García Fandiño wrote:
Hi,
I would like to calculate the PMF of an ion along a channel using
Gromacs 4, and I have a doubt about the options I should use in the .mdp
file:
-which option should I choose for pull_geometry: distance? direction? or
position?
If you're intending on using g_wham to calculate PMF, you must use distance.
-which is the equivalent option to the old "Pos1" (in Gromacs 3) for the
Gromacs 4 version?
Set "pull_start = yes" and "pull_init = 0" to restrain the pull group at the
original COM distance from the reference.
-Justin
Thank you very much for your help.
Best wishes,
Rebeca Garcia Fandiño
Oxford Universtity
UK
------------------------------------------------------------------------
49 habitantes, 49 expertos en Windows 7. Así es Sietes, ¡Visítalo!
<http://www.sietesunpueblodeexpertos.com/>
------------------------------------------------------------------------
_______________________________________________
gmx-users mailing list gmx-users@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-requ...@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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
_______________________________________________
gmx-users mailing list gmx-users@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-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
