[gmx-users] protein wandering away

[Nancy Deng]

Dear All,

I just simulated a 5ns MD by GROMACS FF for a small system containing 160
amino acid residues in a water box. The thing confused me was that the
protein started to close one edge of the water box around 2ns and part of it
movedout of the box later. At the end of the 5ns calculation, most of
protein was out of the box, while water molecules were still in the box.

I use "pbc =xyz", and also other parameters as pasted below for your
opinion. I am just wandering whether I need to re-assign velocity. If so, by
how???  Highly appreciate any of your suggestions.

Nancy

************  the "5ns.mdp" file pasted below************
title               =  5ns
cpp                 =  /usr/bin/cpp
constraints         =  all-bonds
integrator          =  md
dt                  =  0.002    ; ps !
nsteps              =  2500000; 5ns
constraint-algorithm = shake
nstcomm             =  1
nstxout             =  500
nstvout             =  1000
nstfout             =  0
nstlog              =  500
nstenergy           =  500
nstlist             =  10
ns_type             =  grid
coulombtype         =  PME
rlist               =  0.9
rcoulomb            =  0.9
rvdw                =  0.9
fourierspacing      =  0.12
pme_order           =  4
optimize_fft        =  yes
pbc                 = xyz
; Berendsen temperature coupling is on in two groups
Tcoupl              =  berendsen
tc-grps             =   Protein  SOL  CL
tau_t               =   0.1      0.1   0.1
ref_t               =   300      300   300
; Energy monitoring
energygrps          =  Protein SOL  CL
; Pressure coupling is not on
Pcoupl              =  berendsen
pcoupltype          =  isotropic
tau_p               =  1
compressibility     =  4.5e-5
ref_p               =  1
; Generate velocites is on at 300 K.
gen_vel             =  yes
gen_temp            =  300.0
gen_seed            =  173529

******end of attachment*********