[gmx-users] unable to equilibrate protein in membrane with NPT

[Peter C. Lai]

Hello again

In my protein-membrane-water-ion system (inserted via g_membed) I have run 
a 1ns NVT equilibration with the protein restrained and now I am trying to 
equilibrate with NPT and LINCS/mdrun is crashing after about 5000 iterations.

Here is my NPT mdp file:

define                  =-DPOSRES
integrator               = md
; Start time and timestep in ps
tinit                    = 0
dt                       = 0.002
nsteps                   = 500000
init_step                = 0
comm-mode                = Linear
nstcomm                  = 1
comm-grps                = Protein_POPC SOL_CL
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
continuation    = yes
constraint_algorithm = lincs    ; holonomic constraints
constraints     = all-bonds     ; all bonds (even heavy atom-H bonds)
lincs_iter      = 1             ; accuracy of LINCS
lincs_order     = 4             ; also related to accuracy
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     = 0.8
coulombtype     = PME
pme_order       = 4             ; cubic interpolation
fourierspacing  = 0.16          ; grid spacing for FFT
tcoupl          = Nose-Hoover
tc-grps         = Protein POPC SOL_CL
tau-t                    = 0.5 0.5 0.5
ref-t                    = 300 300 300
gen-vel                  = no
pcoupl          = Parrinello-Rahman         ; Pressure coupling on in NPT
pcoupltype      = semiisotropic             ;
tau_p           = 5.0                           ; time constant, in ps
ref_p           = 1.01325 1.01325
compressibility = 4.5e-5        4.5e-5

Any suggestions?
-- 
===============================================================
Peter C. Lai                 | University of Alabama-Birmingham
Programmer/Analyst           | BEC 257
Genetics, Div. of Research   | 1150 10th Avenue South
pcl at uab.edu                  | Birmingham AL 35294-4461
(205) 690-0808               |
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