Parul tew wrote:
Thanks for the reply Justin,
> In theory, that should work. Please post the entirety of your
.mdp file.
Have you done any prior equilibration, or have you moved straight into
annealing? I would suggest a restrained NVT before applying NPT or
annealing
when using the restraints.
Yes I did the restrained NVT before but the same problem came,
morover there was a hole in the upper part of the system with the SOL
molecules displaced. So then I tried to run the annealing but in this
I'm having trouble visualizing this. Is the gap between the lipids and water
molecules, or somewhere else?
case the SOL molecules were intact but similar problem came with the
lipid membrane. though, just to check then I tried to equilibration with
restrained NVT where I restrained the movement of the lipid in all the
x, y, z axis the problem did not occur.
I suppose this will work, although in principle it should not be necessary.
Recall, though, that restraints are only a biasing potential and do not prevent
movement, they simply disfavor it. If a system is wildly far away from
equilibrium, typical restraints can be overcome to some extent.
-Justin
Here is my mdp file
--------------------------------------------------------------------------
title = NVT equilibration for B3-DPPC
define = -DPOSRES -DPOSRES_LIPID ; position restrain the
protein and lipid
; 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 = Protein DPPC SOL_CL- ; three coupling groups - more
accurate
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
; COM motion removal
; These options remove motion of the protein/bilayer relative to the
solvent/ions
nstcomm = 1
comm-mode = Linear
comm-grps = Protein_DPPC SOL_CL-
--------------------------------------------------------------------------
This is the topology file:
--------------------------------------------------------------------------
;Include DPPC chain topology
#include "dppc.itp"
#ifdef POSRES_LIPID
; Position restraint for each lipid
#include "lipid_posre.itp"
#endif
; Include water topology
#include "spc.itp"
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif
; Include generic topology for ions
#include "ions.itp"
[ system ]
; Name
protein
128-Lipid DPPC Bilayer
[ molecules ]
; Compound #mols
Protein_A 1
DPPC 121
SOL 9867
CL- 14
--------------------------------------------------------------------------
thanks
Parul Tewatia
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
