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
-Justin
gyorgy.han...@fc.up.pt wrote:
The mdp file is attached.
Best,
Gyorgy
Quoting "Justin A. Lemkul" <jalem...@vt.edu>:
gyorgy.han...@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.
-Justin
Thanks in advance.
Gyorgy
--
========================================
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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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========================================
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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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