[gmx-users] Re: gmx-users Digest, Vol 89, Issue 107

[Parul tew]

 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 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.



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
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