On 29/04/2012 7:32 PM, Shima Arasteh wrote:
Actually, I am confused somehow.
I want to equilibrate the system. It contains popc and water. To
equilibrate it, using .mdp file I use the nvt.mdp file as below.
title = NVT equilibration for POPC
define = -DPOSRES ; position restrain the protein
; Run parameters
integrator = md ; leap-frog integrator
nsteps = 50000 ; 2 * 50000 = 100 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) constrained
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 = 1.2 ; short-range neighborlist cutoff (in nm)
rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm)
rvdw = 1.2 ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range
electrostatics
pme_order = 4 ; cubic interpolation
fourierspacing = 0.16 ; grid spacing for FFT
; Temperature coupling is on
tcoupl = V-rescale ; modified Berendsen thermostat
tc-grps = POPC SOL ; two coupling groups - more accurate
Here you instruct grompp to expect the POPC group...
tau_t = 0.1 0.1 ; time constant, in ps
ref_t = 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
I enter this command:
# grompp -f nvt.mdp -c em.gro -p popc.top -o nvt.tpr
Getting this fatal error:
Group POPC not found in index file.
Group names must match either [moleculetype] names
or custom index group names,in which case you
must supply an index file to the '-n' option of grompp.
I don't need index file, do I? What is the problem with my .mdp file?
... but POPC is not defined implicitly by your .top+.gro combination,
nor explicitly in an index file supplied with grompp -n. AFAIK if your
[moleculetype] is named POPC then it is all OK, but maybe the fact that
your .gro file has the POPC "residues" named POP is confusing that
mechanism. As you can see with your earlier example with make_ndx, the
POP group is defined implicitly by the residue names in your .gro file,
so if you use that output index file and reference POP in your .mdp
file, all will be good. You might get away without using that index
file, but I am not sure about this. Simpler still is to use Water and
non-Water as your T-coupling groups, but this will need changing if down
the road you need Protein as well (or such).
Mark
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