[gmx-users] angle constrain, constrained PF6 anion
Justin A. Lemkul
jalemkul at vt.edu
Tue Feb 1 20:01:47 CET 2011
There's at least one problem that I see:
dt = 0.00000001 ! just to see if it starts
This line won't be parsed properly. Check your mdout.mdp to see what grompp is
assigning as a value for dt. You shouldn't need to set a value this small to
see if it's going to work or not, anyway.
It would also be useful to know what sort of minimization and equilibration
you've done prior to this step, since most cases of the system collapsing are
generally attributed to one of three problems:
1. Poor starting geometry/insufficient minimization and/or equilibration
2. Bad parameters
3. Incorrect .mdp settings
gyorgy.hantal at fc.up.pt wrote:
> The mdp file is attached.
> Quoting "Justin A. Lemkul" <jalemkul at vt.edu>:
>> gyorgy.hantal at fc.up.pt wrote:
>>> Dear all,
>>> I am setting up a simulation of ionic liquids with the PF6 anion.
>>> According to the potential, the anion should be kept rigid, wich
>>> obviously means that bond lengths and angles have to be constrained.
>>> LINCS doesn't work with angle constraints (i.e. constraing a
>>> triangle), so we decided to use SHAKE. However, SHAKE seems to work
>>> a bit strangely: I know SHAKE mustn't be used with domain
>>> decomposition, but even if I set the corresponding variable to NO in
>>> the mdp file, the simulation crashes on 8 procs and gives the
>>> following error message:
>>> Fatal error:
>>> 1 particles communicated to PME node 7 are more than a cell length
>>> out of the domain decomposition cell of their charge group.
>>> If I try to run mdrun with -pd (to 'really' switch off domain
>>> decomposition), the simulation doesn't chrash but gives nonsense
>>> (the energy seems to increase constantly).
>>> I am not an expert user so maybe I do something wrong but, anyway,
>>> does anyone have an idea how to constrain this anion with Gromacs? I
>>> checked mailing list archive but couldn't find any answer
>>> corresponding to my question.
>> Without seeing a complete .mdp file, it's not possible to fully
>> diagnose this problem. The combination of SHAKE + particle
>> decomposition should be stable, but there are a whole host of different
>> things that can go wrong.
>>> Thanks in advance.
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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