Mark Abraham wrote:
Nuri A Temiz wrote:
Dear Mark
The mdp file is how it should be. I also did a cut-off run from the
same starting point and it runs. For the PME i have tried to decrase
the time step to 1 fs. that did not work
either. The protein is exploding and simulations is crashing.
OK. Take your cutoff and PME .tpr files and compare them. The simplest
thing to do is to "gmxdump -s cutoff.tpr > cutoff.txt" and similarly for
PME. Then use diff to compare them. This will make absolutely clear
whether you are doing the same thing with different electrostatic
treatment or not. Also visualize the exploding and non-exploding runs to
see if that enlightens you.
You can do this in one go using:
gmxcheck -s1 cutoff -s2 pme | less
Mark
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
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
--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
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
