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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