[gmx-users] problem about distance restraint in REMD simulation
曾娟
zengjuan at pkusz.edu.cn
Sun Jun 12 11:58:45 CEST 2016
Dear Users:
I have a system with four distance restraints to maintain a hydrogen-bonding network in REMD simulation. While when I applied the distance restraint, the REMD simulation is only ok when applied single CPU for each replica. When I applied more than one CPU for each replica, there are error message like this: "Time or ensemble averaged or multiple pair distance restraints do not work (yet) with domain decomposition, use particle decomposition (mdrun option -pd)". But the "-pd" option can not solve the problem. I have also read some archives, but still unknow how to solve the problem. Can you give me some advices. Thanks!
My file added distance restraint is:
; distance restraints for r_46_&_N_or_r_50_&_O of Protein in water
[ distance_restraints ]
; i j ? label funct lo up1 up2 weight
409 467 1 0 1 0.210000 0.390000 0.50000 1
421 464 1 1 1 0.210000 0.390000 0.50000 1
423 440 1 2 1 0.210000 0.390000 0.50000 1
425 447 1 3 1 0.210000 0.390000 0.50000 1
And my mdp file is :
cpp = /usr/bin/cpp
integrator = md
define = -DPOSRES
dt = 0.0025
nsteps = 600000000
constraints = hbonds
disre = simple
disre-fc = 1000
nstxout = 0
nstvout = 0
nstxtcout = 600
xtc_grps = Protein
nstlog = 600
nstenergy = 600
nstlist = 5
ns_type = grid
rlist = 0.9
coulombtype = PME
rcoulomb = 0.9
vdwtype = cut-off
rvdw = 0.9
DispCorr = EnerPres
Tcoupl = v-rescale
tc_grps = system
tau_t = 0.2
ref_t = 290.0
Pcoupl = no
gen_vel = no
Juan
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