Hi there,
I haven't found a post describing this problem, so here I am.
I'm running GROMACS 4.3.5 with the OPLS-AA force-field and the TIP3P
water model on a 170kDa protein dimer with sodium ions to neutralize the
charges. I added two new residues to the force-field (which seem to
behave normally). Now the problem:
When I run with domain decomposition everything works fine during 9ns.
The structure seems to equilibrate more or less and the overall domain
conformation doesn't seem to alter much.
When I switch on particle decomposition, however, the simulation crashes
after 2-3ns due to a lincs warning. It seems to happen always at the
same residue, Arg318 which gets pulled/pushed out of the helix it is in.
The closest modified residue is 326 which doesn't seem to be disturb the
system too much.
Anyway it seems strange to me that the method of decomposition seems to
change the outcome of the simulation a lot (and does not only reflect in
the computing time). Now I don't understand too much of the algorithms
used. And as I couldn't find anything bout adjusting parameters if using
the one or the other I'm a bit in the dark about what to do now.
Did you have similar experiences? How do you suggest that I tackle the
problem? Do you need more information? In case it is of any relevance
here the parameters of the mdp file:
dt = 0.002
nsteps = 1500000
comm-grps = system
nstxout = 20000
nstvout = 20000
nstfout = 20000
nstlog = 20000
nstcalcenergy = 1
nstxtcout = 500
xtc-grps = protein
energygrps = protein
ns_type = grid
rlist = 1.0
coulombtype = PME
vdw-type = Cut-off
rcoulomb = 1.0
rvdw = 1.0
DispCorr = EnerPres
tcoupl = V-rescale
tc-grps = Protein Non-Protein
tau_t = 0.1 0.1
ref_t = 325 325
pcoupl = Parrinello-Rahman
pcoupltype = isotropic
tau_p = 2.0
compressibility = 4.5e-5
ref_p = 1.0
andersen_seed = -1
gen_vel = no
gen-temp = 325
gen-seed = -1
constraints = all-bonds
constraint_algorithm = lincs
continuation = yes
lincs_order = 4
lincs_iter = 1
disre = simple
disre_weighting = conservative
disre_fc = 800
disre_tau = 0
Thank you very much.
Regards,
Florian
--
Florian Altvater
Albert-Ludwigs-Universität Freiburg
Institut für Physikalische Chemie - Lehrstuhl I
Albertstr. 21
79104 Freiburg, Germany
Phone: +49 (761) 203-6210
Fax: +49 (761) 203-6222
E-Mail: florian.altva...@physchem.uni-freiburg.de
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