[gmx-users] Blowing up a 512 dodecanol system ..

Dallas Warren dallas.warren at monash.edu
Tue Oct 16 00:39:59 CEST 2018

" For example, two hydrogens in one
methylene group became very close and even they overlap each other. After
one or two steps from this event the system blows up."

Is it the same hydrogen bonds overlapping, in different molecules or
parts of the molecule?  I would be looking at the group of angle
parameters around those centers, there would be a total of 6 for the
CH3 section.  Probably an improper dihedral too.  Though that all does
depend a bit on the FF, and how it works, no experience with GAFF

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
When the only tool you own is a hammer, every problem begins to resemble a nail.
On Mon, 15 Oct 2018 at 23:32, Sergio Garay
<sergio.alberto.garay at gmail.com> wrote:
> Dear Gromacs Users
> I've prepared a 1-dodecanol system based on an 1-octanol-GAFF topology
> taken from:
> http://virtualchemistry.org/molecule.php?filename=1-octanol.zmat
> I've run a minization of one dodecanol and also a box with 512 molecules
> without any visible problem. I did not find any weird distance, angle o
> dihedral angle.
> The problem starts when I try to run a NVT simulation because the system
> blows up. I have watched the time evolution (VMD) of the system every 2 fs
> (because it blows up at the very beginning), I could see that most of the
> molecules have a proper conformation, but one of them suffers a dramatic
> (no sense) conformational change. For example, two hydrogens in one
> methylene group became very close and even they overlap each other. After
> one or two steps from this event the system blows up.
> I've tried with no success:
> * I have read the gromacs web page where it is described all the details to
> take into account when a Blowing up happen (
> http://www.gromacs.org/Documentation/Terminology/Blowing_Up)
> * Check the topology file, looking carefully for some missing term
> * Decrease the temperature of the simulation.
> * Increase the temperature coupling time
> * Decrease the integration time step
> I've run several times this system and the molecule which blows up is
> always different, but the rest of the molecules look healthy (no weird
> conformation).
> I need an equilibrated box of dodecanol (compatible with Amber forcefield)
> in order to run a simulations of one the molecules that I am interested in.
> Any help will be very appreciated.
> --
> *Sergio GarayDr. en Ciencias BiológicasFacultad de Bioquimica y Cs.
> BiológicasUniversidad Nacional del LitoralSanta Fe - ArgentinaC.C. 242 -
> Ciudad Universitaria - C.P. S3000ZAAArgentinaPh. +54 (342) 4575-213Fax. +54
> (342) 4575-221 *
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