On 4/28/15 8:14 AM, Abhijit Jassem wrote:
Hi all,
I am a beginner to GROMACS and MD simulations in general. I’m trying to
model electroporation in a DPPC membrane but I am having issues with the
energy minimization step. I am basing my approach on the one followed in
Dr. Justin Lemkul’s KALP-15 in DPPC Tutorial (
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html)
but without the steps that use the KALP peptide. After I solvate my
membrane, I am trying to run energy minimization, but my steps are moving
much slower than normal and I get the error Water molecule starting at
atom 109448 can not be settled. Check for bad contacts and/or reduce the
Well, what's going on around atom 109448?
timestep if appropriate.” When I looked this error up, I found that
this suggested that I had a bad starting structure, possibly with atoms
overlapping. Based on this, I assume this error originates when I solvate
my membrane. I am currently using the spc216.gro model. Is this an issue
with my water model or am I doing something else wrong?
There are plenty of potential problems, unfortunately not enough information to
go on. Simply using SPC isn't a problem, but something either in the
configuration or the force field is an issue. Rather than building a large
system (you have over 100,000 atoms), do something small, like the pre-built
DPPC bilayer that the tutorial uses. That's a sanity check. If that minimizes
and equilibrates well, that means the force field is fine and something is wrong
with the way you built your larger system. If you want help with that, you have
to tell us exactly what you're doing (exact command sequence).
-Justin
--
==
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==
--
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.
