Dear all,
I am doing simulation of membrane protein for this I am
following justin's tutorial In the first equilibration step i am getting
error like this-
-------------------------------------------------------
Program mdrun, VERSION 4.0.3
Source code file: trnio.c, line: 252
File input/output error:
Cannot write trajectory frame; maybe you are out of quota?
Can anyone have idea to solve this problem? If have please let me know.
My command line like this-
mdrun -v -s nvt.tpr -o new_seq-nvt.trr -c new_seq-nvt.gro -e
newe_seq-nvt.edr -g new_seq-nvt.log.
My nvt.mdp file is below-
title = NVT equilibration for TAP-DMPC
define = -DPOSRES ; position restrain the protein
; Run parameters
integrator = md ; leap-frog integrator
nsteps = 25000 ; 2 * 25000 = 50 ps
dt = 0.002 ; 2 fs
; Output control
nstxout = 100 ; save coordinates every 0.2 ps
nstvout = 100 ; save velocities every 0.2 ps
nstenergy = 100 ; save energies every 0.2 ps
nstlog = 100 ; update log file every 0.2 ps
; Bond parameters
continuation = no ; first dynamics run
constraint_algorithm = lincs ; holonomic constraints
constraints = all-bonds ; all bonds (even heavy atom-H bonds)
constrai
ned
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
ns_type = grid ; search neighboring grid cels
nstlist = 5 ; 10 fs
rlist = 1 ; short-range neighborlist cutoff (in nm)
rcoulomb = 1 ; short-range electrostatic cutoff (in nm)
rvdw = 1.2 ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = cut-off ; coulombtype cut-off
pme_order = 4 ; cubic interpolation
fourierspacing = 0.16 ; grid spacing for FFT
; Temperature coupling is on
tcoupl = V-rescale ; modified Berendsen thermostat
tc-grps = Protein DMPC SOL_NA+ ; three coupling groups - more
accurat
e
tau_t = 0.1 0.1 0.1 ; time constant, in ps
ref_t = 323 323 323 ; reference temperature, one for
each
group, in K
; Pressure coupling is off
pcoupl = no ; no pressure coupling in NVT
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
; Dispersion correction
DispCorr = EnerPres ; account for cut-off vdW scheme
; Velocity generation
gen_vel = yes ; assign velocities from Maxwell
distribution
gen_temp = 323 ; temperature for Maxwell distribution
gen_seed = -1 ; generate a random seed
Thanks a lot in advance.
Nitu sharma
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