[gmx-users] Simulations with Verlet scheme, virtual sites and heterogeneous systems

[Mark Abraham]

On Mon, Apr 27, 2015 at 12:26 PM, Ivan Gladich <igladich at sissa.it> wrote:

> Dear Gromacs users,
>         I am experiencing a strange behavior using Verlet-cutoff scheme in
> combination with a water model with virtual sites.
> I am simulating an ice slab with NE6 water model. NE6 water model is used
> for simulation of ice and it consists of 3 atom sites and 3 virtual sites.
> My system has two vacuum interfaces as drawn below.
>
> ------------|------------|---------
> vacuum  | ice         |  vacuum
>                |               |
> -------------------------------
>
> My simulation run at 240 K and, at this temperature, my ice should not
> melt (for this water model Tm=289 K).
> Using a group scheme , my ice remains stable over 10 ns
>
> cutoff-scheme   = group
> ns_type             = grid
> nstlist                 = 1
> rlist                   = 1
> pbc                    = xyz
> rcoulomb                 = 1.0
> vdw-type                 = Cut-Off
> rvdw                     = 1.0
>
> *
> **On the contrary*, using a Verlet cut-off scheme
>
> cutoff-scheme   = Verlet
> ns_type         = grid
> nstlist         = 10
> pbc             = xyz
> vdw-type                 = Cut-Off
> rvdw                     = 1.0
>
> I start to observe that
> 1) sometimes  my ice suddenly (not in a realist way) melts after ~7 ns and
> my simulation crashes
> OR
> 2) some particle are kicked out with high velocity and my run crashes with
> this message
>
> -------------------------------------------------------
> Program mdrun_4_7_gpu_s, VERSION 4.6.7
> Source code file: /home/igladich/opt/gromacs-4.6.7/src/mdlib/pme.c, line:
> 851
>
> Fatal error:
> 2 particles communicated to PME node 0 are more than 2/3 times the cut-off
> out of the domain decomposition cell of their charge group in dimension y.
> This usually means that your system is not well equilibrated.
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
>
>
> I am uploading the temperature profile and the *.mdp file at
>
> http://goo.gl/0zfqfe
>
> So, my questions concern the Verlet scheme
> 1) Can  this scheme  properly work in the presence of an heterogeneous
> system as mine (with an interface on vacuum)?
>

Most certainly - we use it for a water droplet in vacuum falling onto a
surface, for example. There's nothing about the implementation that cares
about heterogeneity.


> 2) Can the problem be the virtual sites in  my water models? Because I
> saw, running  grompp the following note...
>
> NOTE 2 [file grompp-RUN-NE6-4_7.mdp]:
>   There are 5760 non-linear virtual site constructions. Their contribution
>   to the energy drift is approximated. In most cases this does not affect
>   the energy drift significantly.
>

Perhaps. How well does your model actually do at reproducing (say) bulk
water properties under the various conditions?

I can't recall if there's been a relevant vsites bug fix since 4.6, but you
could try 5.0.4 also.

Mark


> 3) Is there a way to go around this issue?  With GPU+Verlet and I doing
> ~110 ns/day while, with group+CPU 33 ns/day ....
>
> Thanks for any possible help or suggestions
> Sincerely
> Ivan
>
>
> --
> ------
> Ivan Gladich, Ph.D.
> Research Assistant
> International School for Advanced Studies (SISSA)
> Via Bonomea 265, I-34136, Trieste,
> Italy
>
> Room: 331
> Tel: +390403787335
> e-mail:igladich at sissa.it
> web page:http://people.sissa.it/~igladich/
>
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