Shay Amram wrote:
Of course. I'm using version 3.3.3 of GROMACS.
-Shay
Is this reproducible?
You could try to fork off a tpr file using tpbconv -f -e -s -o just
before this happens and rerun it.
It can also be combined by input parameters, e.g. too large time step,
too infrequent neighborsearching etc., use of cutoffs.
-----Original Message-----
From: [email protected] [mailto:[email protected]]
On Behalf Of Mark Abraham
Sent: Tuesday, December 30, 2008 02:59 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Forces are large - How to track down the culprit
Shay Amram wrote:
Greetings dear Gromacs users,
I have recently been simulating a POPG membrane* in water (SPC). Several
of my simulations after running well into the 10ns and 20ns are
sometimes getting a "Forces for atom X are large".
I'm rather unsure as to the cause of this situation. Moreover, as far as
I can tell from viewing the simulation, the system _does NOT_ explode
(as may be suggested by wiki.gromacs and some previous answers to this
kind of situation). The rest of the simulation looks much as it did in
the beginning.
I would be interested (and thankful!) to hear any of your opinions as to
why I'm getting this message (or how to catch the culprit), and more
importantly, how to prevent it from happening in the future.
During this version-transitive period, it's always right to report the
GROMACS version that you're using. It would normally be right to be
using the most recent version (4.0.2) if encountering problems.
Mark
_______________________________________________
gmx-users mailing list [email protected]
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 [email protected].
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
_______________________________________________
gmx-users mailing list [email protected]
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 [email protected].
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
[email protected] [email protected] http://folding.bmc.uu.se
_______________________________________________
gmx-users mailing list [email protected]
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 [email protected].
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
