[gmx-users] parameters problem

[Nidhi Katyal]

Dear all

I am trying to simulate a protein in 3 steps: energy minimization (using
em.mdp), position restraints (using pr.mdp) and final production run by NPT
ensemble (using full.mdp) at 300K

At this temperature, it is known by previous literature survey that protein
keeps its secondary structure almost intact. But according to my
simulations (done thrice), protein starts loosing its secondary structure
around 6-8ns only. I have used the following parameters:

*em.mdp*

;
;     User spoel (236)
;     Wed Nov  3 17:12:44 1993
;     Input file
;
cpp                 =  /usr/bin/cpp
define              =  -DFLEX_SPC
constraints         =  none
integrator          =  steep
nsteps              =  250000
;
;     Energy minimizing stuff
;
emtol               =  2000
emstep              =  0.001

nstcomm             =  1
ns_type             =  grid
rlist               =  1
rcoulomb            =  1.0
rvdw                =  1.0
Tcoupl              =  no
Pcoupl              =  no
gen_vel             =  no


*pr.mdp*

;
;     User spoel (236)
;     Wed Nov  3 17:12:44 1993
;     Input file
;
title               =  Yo
cpp                 =  /usr/bin/cpp
define              =  -DPOSRES
constraints         =  all-bonds
integrator          =  md
dt                  =  0.002  ; ps !
nsteps              =  50000  ; total 100 ps.
nstcomm             =  1
nstxout             =  5000
nstvout             =  5000
nstfout             =  0
nstlog              =  10
nstenergy           =  10
nstlist             =  10
ns_type             =  grid
rlist               =  1.0
rcoulomb            =  1.0
rvdw                =  1.0
; Berendsen temperature coupling is on in two groups
Tcoupl              =  berendsen
tc-grps               =  Protein    Non-protein
tau_t               =  0.1    0.1
ref_t               =  300    300
; Energy monitoring
energygrps      =  Protein    Non-protein
; Pressure coupling is not on
Pcoupl              =  no
tau_p               =  0.5
compressibility     =  4.5e-5
ref_p               =  1.0
; Generate velocites is on at 300 K.
gen_vel             =  yes
gen_temp            =  300.0
gen_seed            =  173529


*full.mdp*

;
;     User spoel (236)
;     Wed Nov  3 17:12:44 1993
;     Input file
;
title               =  Yo
cpp                 =  /usr/bin/cpp
constraints         =  all-bonds
integrator          =  md
dt                  =  0.002  ; ps !
nsteps              = 25000000      ; total 50000 ps.
nstcomm             =  1
nstxout             =  5000
nstvout             =  5000
nstfout             =  0
nstlog              =  5000
nstenergy           =  5000
nstlist             =  10
ns_type             =  grid
rlist               =  1.0
rcoulomb            =  1.0
rvdw                =  1.0
; Berendsen temperature coupling is on in two groups
Tcoupl              =  berendsen
tc-grps               =  Protein Non-protein
tau_t               =  0.1    0.1
ref_t               =  300      300
; Energy monitoring
energygrps          =  Protein  Non-protein
; Isotropic pressure coupling is now on
Pcoupl              =  berendsen
Pcoupltype          = isotropic
tau_p               =  0.5
compressibility     =  4.5e-5
ref_p               =  1.0
; Generate velocites is off at 300 K.
gen_vel             =  no
gen_temp            =  300.0
gen_seed            =  173529

 I don't think it is the problem of thermostat because even after using
V-rescale for temperature coupling and Parinello Rahman for pressure
coupling, my protein loses its secondary structure in the initial time of
simulation.

Also, I have carried out various checks (like potential energy convergence
after em, temperature check after pr, and pressure and density check after
full), all of which seems to converge well.

Please help me figure out the problem.