On 6/4/13 11:47 PM, Shima Arasteh wrote:
Dear gmx users,
I have a POPC/peptide/water/ions system. I ran NVT and then NPT on my system.
I'd prefer to run the equilibrium steps with position restraints on water
oxygen atoms, because the water molecules penetrate the lipid bilayer when
running the equilibrium and I don't want it to happen.
I tried the NVT with position restraints on water by adding -DPOSRES_WATER to
nvt.mdp file and editing the top file by changing the fc to 100000.
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 100000 100000 100000
#endif
This edition turned into a better result.
Now I tried to put such a restraint on npt but the gromacs does not allow it by
turning a fatal error:
A charge group moved too far between two domain decomposition steps.
npt.mdp file:
;NPT equlibration Dimer-POPC-Water - CHARMM36
define = -DPOSRES_LIPID -DPOSRES -DPOSRES_WATER ; P headgroups of
POPC and Protein is position restrained (uses the posres.itp file information)
integrator = md ; leap-frog integrator
nsteps =1000000 ; 1 * 1000000 = 1000 ps
dt = 0.001 ; 1 fs
; Output control
nstxout = 2000 ; save coordinates every 0.2 ps
nstvout = 1000 ; save velocities every 0.2 ps
nstenergy = 1000 ; save energies every 0.2 ps
nstlog = 1000 ; update log file every 0.2 ps
continuation = yes ; first dynamics run
constraint_algorithm = lincs ; holonomic constraints
constraints = h-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 cells
nstlist = 5 ; 10 fs
rlist = 1.2 ; short-range neighborlist cutoff (in nm)
rlistlong = 1.4
rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm)
rvdw = 1.2 ; short-range van der Waals cutoff (in nm)
vdwtype = switch
rvdw_switch = 1.0
; 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 = Nose-Hoover ; modified Berendsen thermostat
tc-grps = Protein_POPC Water_Ces_CL ; two coupling groups - more
accurate
tau_t = 0.5 0.5 ; time constant, in ps
ref_t = 310 310 ; reference temperature, one for each group, in K
pcoupl = Berendsen ; no pressure coupling in NVT
pcoupltype = semiisotropic
tau_p = 4
ref_p = 1.01325 1.01325
compressibility = 4.5e-5 4.5e-5
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
; Velocity generation
gen_vel = no ; assign velocities from Maxwell distribution
;gen_temp = 310 ; temperature for Maxwell distribution
;gen_seed = -1 ; generate a random seed
nstcomm = 1
comm_mode = Linear
comm_grps = Protein_POPC Water_Ces_CL
refcoord_scaling = com
I am wondering how it is possible to prevent penetrating the water molecules
through equilibrium? And how I can put the restraint in npt as well as nvt?
Would you please help me in this issue please?
Restraints in all directions, especially with pressure coupling, will
undoubtedly lead to nasty atomic clashes and the failure that you're seeing.
Normally, one does not need to apply restraints in any other dimension aside
from z, to prevent "vertical" diffusion into the membrane. The structure of the
membrane should be reasonable after NVT; if it's not, it suggests a poor
starting configuration. Occasional water leakage is one thing, having to
completely restrain water molecules to prevent it from happening suggests
something is very bad.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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