On 4/10/20 4:17 PM, Alex wrote:
On Fri, Apr 10, 2020 at 9:19 AM Justin Lemkul <jalem...@vt.edu> wrote:
On 4/10/20 9:16 AM, Alex wrote:
Thank you for the response.
On Fri, Apr 10, 2020 at 9:02 AM Justin Lemkul <jalem...@vt.edu> wrote:
On 4/10/20 8:13 AM, Alex wrote:
Dear Justin,
Any comment please?
Sorry, haven't had power/network for a while due to some bad storms
here.
GROMOS force fields are parametrized assuming all bonds are fixed, so
your constraints should be "all-bonds" not "h-bonds."
Interesting, hopefully that is the problem.
By constraining all the bonds "constraints = all-bonds", the simulation
crashes in the first step immediately irrespective to the starting point of
simulation, even if I continue the old working simulation.
Now we're getting somewhere. That suggests that at least one bond has
deviated substantially from its equilibrium length, such that the
constraint algorithm fails immediately. This also likely underlies the
original failure - forces are building up on some atoms such that mdrun
crashes.
You have either a bad geometry, inadequate topology, or both. Inspect
the molecule(s) that mdrun complains about to see if the molecules are
distorted by computing bond lengths and comparing against the force
field's parameters.
It may be beneficial to re-minimize and equilibrate with the proper
constraint scheme after validating that the topology is of sufficient
quality.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall
Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com
==================================================
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
mail to gmx-users-requ...@gromacs.org.
