[gmx-users] Implementation of drude simulation
jalemkul at vt.edu
Mon Nov 26 15:51:22 CET 2018
On 11/22/18 9:37 AM, Gonzalo Quezada wrote:
> Greetings gromacs users,
> I'm trying to run a simulation of polarizable water and ions with the
> drude-2013 forcefield. I use the simulation parameters from the supporting
> information from "Implementation of Extended Lagrangian Dynamics in GROMACS
> for Polarizable Simulations Using the Classical Drude Oscillator Model".
Please note that this implementation remains developmental and therefore
is not officially supported yet. Most features work but I still haven't
completed the domain decomposition code re-write.
> In pure water (SWM4-NDP) I have no issues, but when I incorporate ions like
> Na and Cl most of the simulation crash. Also, the message of HARDWALL
> appear at every step for the ions. I studied the simulations to find when
> and how the crash is produce but without success because the reasons are
> not sistematic.
If you're trying to run with DD, then these failures are spurious. If
you're using OpenMP to parallelize, then you probably haven't adequately
minimized/equilibrated the system. It is extremely easy to break a
polarizable simulation, particularly in the early stages.
> I'm still learing so I think maybe the simulations parameters that I put
> are not the best suitable for ions.
You haven't given any useful diagnostic information, such as what steps
you've taken or what input settings you're using, so there's not much to
go on to help you.
Justin A. Lemkul, Ph.D.
Office: 301 Fralin Hall
Lab: 303 Engel Hall
Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
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