Hi,
The exclusions in the topology introduce long range interactions
that require large domain decomposition cells.
The md.log of 4.0.3 will tell you this.
Remove all those exclusions and add energygrp exclusions in the mdp file.
(Or do not use exclusions at all)
Berk
Date: Thu, 22 Jan 2009 12:37:24 -0800
From: resa...@yahoo.com
To: gmx-users@gromacs.org
Subject: [gmx-users] Domain Decomposision and Frozen Groups
Hi everyone;
I am trying to do some simulation using frozen groups on an 8 core computer. I
have tow boxes:
1) Box 1 has two proteins and both of them are kept frozen (I used [exclusions]
directive in topology file to exclude the interactions in each frozen group,
NVT).
2) Box 2 has those two proteins but without being frozen (no use of
[exclusions] and freeze options).
Here is the mdp file:
=========================================================
integrator = sd
dt = 0.002
nsteps = 50000
comm_mode =
None
ns_type = grid
pbc = xyz
nstlist = 10
rlist = 1
coulombtype = PME
rcoulomb = 1
fourierspacing = 0.12
pme_order = 6
ewald_rtol = 1e-6
vdwtype = Switch
rvdw_switch = 0.8
rvdw = 0.9
DispCorr = EnerPres
nstxout =
500
nstvout = 500
nstlog = 500
nstenergy = 500
nstxtcout = 5000
xtc-precision = 1000
tc_grps = system
tau_t = 1
ref_t = 310
energygrps = chainC chainF SOL ; these three lines were commented out for
the box 2 simulation
freezegrps = chainC
chainF
freezedim = Y Y Y Y Y Y
=========================================================
I used this command to run the simulations:
mpiexec -n 8 mdrunmpi -s eqvspc.tpr -c eqvspc.gro -o eqvspc.trr -x eqvspc.xtc
-g eqvspc.log -e eqvspc.edr
It works for the box two (no freeze), but for box 1 gives me this error:
=========================================================
Back Off! I just backed up eqvspc.log to ./#eqvspc.log.11#
Reading file eqvspc.tpr, VERSION 4.0.3 (single precision)
-------------------------------------------------------
Program mdrunmpi, VERSION 4.0.3
Source code file: domdec.c, line: 5858
Fatal error:
There is no domain decomposition for 8 nodes that is compatible with the given
box and a minimum cell size of 6.25692 nm
Change the number of nodes or mdrun option -rdd or -dds
Look in the log file for details on the domain
decomposition
-------------------------------------------------------
Error on node 0, will try to stop all the nodes
Halting parallel program mdrunmpi on CPU 0 out of 8
==========================================================
The serial version of mdrun works with box 1.
I searched the user mailing list and found that some people had similar problem
with restraints in the past. I tried to use some -rdd and -dds values, but
without any success. Can you please point out where is the source of this error
and how I can get domain decomposition and frozen (or restraint) groups to work.
Any help or hint is highly appreciated!
Reza Salari
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