Ozlem Ulucan wrote:
Dear Justin,
Thanks for the fast response. The exact command I used is :
mdrun -v -s eq2.tpr -deffnm eq2 -g eq2.log -nice 19 >& eq2.out &
This is for a serial run. There's no problem with this (except that -s and -g
are redundant with -deffnm, but that's not an issue). What about your command
for the parallel run?
-Justin
Regards,
Ozlem
On Wed, May 4, 2011 at 3:23 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
Ozlem Ulucan wrote:
Dear Gromacs Users,
I have been trying to simulate a protein in implicit solvent.
When I used a single processor by setting -nt to 1 , I did not
encounter any problem. But when I tried to run the simulations
using more than 1 processor I get the following error.
Fatal error:
Constraint dependencies further away than next-neighbor
in particle decomposition. Constraint between atoms 2177--2179
evaluated
on node 3 and 3, but atom 2177 has connections within 4 bonds
(lincs_order)
of node 1, and atom 2179 has connections within 4 bonds of node 3.
Reduce the # nodes, lincs_order, or
try domain decomposition.
I set the lincs_order parameter in .mdp file to different
values. But it did not help. I have some questions regarding
the information above.
1) Is it possible to run implicit solvent simulations in parallel?
Yes.
2) As far as I know gromacs uses domain decomposition as
default. Why does in my simulations gromacs use the particle
decomposition which I do not ask for.
Without seeing the exact commands you gave, there is no plausible
explanation. DD is used by default.
-Justin
Any suggestions are appreciated very much.
I am ussing gromacs-4.5.4 with charmm force field and the OBC
implicit solvent model. If you need further informations,
probably a run input file, let me know.
Regards,
Ozlem Ulucan
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
<tel:%28540%29%20231-9080>
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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