Hi all,
I am trying to use a simple scheme to restrain a few distances within my
protein, which is contained within an octahedral box of SPC water.
In place of distance restraints, I'm using bond type 6 to utilize a harmonic
potential to restrain the distance between a few atoms. When I imposed one such
restraint in the topology, the simulation ran fine. After finishing this
trajectory, I wanted to impose a second restraint and try again. At this point,
the simulation fails with the following:
mpirun -np 24 mdrun_4.0.2_gcc_mpi -s nvt.tpr -deffnm nvt
<snip>
Initializing Domain Decomposition on 24 nodes
Dynamic load balancing: auto
Will sort the charge groups at every domain (re)decomposition
Initial maximum inter charge-group distances:
two-body bonded interactions: 1.634 nm
multi-body bonded interactions: 0.606 nm
Minimum cell size due to bonded interactions: 1.797 nm
Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.876 nm
Estimated maximum distance required for P-LINCS: 0.876 nm
Guess for relative PME load: 0.45
Will use 12 particle-particle and 12 PME only nodes
This is a guess, check the performance at the end of the log file
Using 12 separate PME nodes
Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
Optimizing the DD grid for 12 cells with a minimum initial size of 2.246 nm
The maximum allowed number of cells is: X 2 Y 2 Z 2
-------------------------------------------------------
Program mdrun_4.0.2_gcc_mpi, VERSION 4.0.2
Source code file: domdec.c, line: 5842
Fatal error:
There is no domain decomposition for 12 nodes that is compatible with the given
box and a minimum cell size of 2.24633 nm
Change the number of nodes or mdrun option -rdd or -dds
Look in the log file for details on the domain decomposition
-------------------------------------------------------
"I'm Only Faking When I Get It Right" (Soundgarden)
I realize there are more optimizations I could impose to better balance the
PP/PME load. I have tried those (altering my cutoff's and grid spacing) but it
makes no difference. Plus, I'd like to remain consistent with the original
simulation that used only one restraint. If I remove the second restraint, the
simulation runs just fine. For reference, the restraints I'm imposing are:
330 1016 6 0.669 5.0300e+06
1016 559 6 0.376 5.0300e+06
The box vectors from the .gro file are:
7.14132 6.73290 5.83086 0.00000 0.00000 2.38044 0.00000
-2.38044 3.36645
Is there anything obvious that I'm doing wrong? Or should I just use real
distance restraints, according to manual section 4.3.4? Thanks for any insights.
-Justin
--
========================================
Justin A. Lemkul
Graduate Research Assistant
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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