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

[Ivan Gladich]

Dear Mark
        thanks for your reply.
As you suggested, I will try with the version 5.0.4
and I will test the setup this water model with Verlet and in bulk water.
I will keep you posted

Ivan

On 04/27/2015 03:04 PM, Mark Abraham wrote:
> 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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-- 
------
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/