[gmx-users] Hello

[Anik Sen]

Dear Sir/madam,
                               Below is a .mdp file for running the equilibration of my protein sample in water. I am using temperature coupling as well as pressure coupling. This indicates of doing a NPT ensemble, right??

For NVT ensemble, what should i do, just do a temperature coupling?

Please let me know,,,,

Anik Sen

 title             =  trp_drg
warning             =  10
cpp                 =  /usr/bin/cpp
define              =  -DPOSRES
constraints         =  all-bonds
integrator          =  md
dt                  =  0.001 ; ps !
nsteps              =  250000 ; total 500.0 ps.
nstcomm             =  100
nstxout             =  250 ; ouput coordinates every 0.5 ps
nstvout             =  1000 ; output velocities every 2.0 ps
nstfout             =  0
nstlog              =  100
nstenergy           =  100
nstlist             =  100
ns_type             =  grid
rlist               =  1.0
coulombtype         =  PME
rcoulomb            =  1.0
vdwtype             =  cut-off
rvdw                =  1.0
fourierspacing      =  0.12
fourier_nx          =  0
fourier_ny          =  0
fourier_nz          =  0
pme_order           =  6
ewald_rtol          =  1e-5
optimize_fft        =  yes
; V-rescale temparature coupling is on
Tcoupl              =  V-rescale
tau_t               =  1.0    0.0
tc_grps             =  SOL   protein
ref_t               =  300    300
; Pressure coupling is on
pcoupl              =  berendsen ; Use Parrinello-Rahman for research work
pcoupltype          =  isotropic ; Use semiisotropic when working with membranes
tau_p               =  2.0
compressibility     =  4.5e-5
ref_p               =  1.0
refcoord-scaling    =  all
; Generate velocites is on at 300 K.
gen_vel             = yes
gen_temp            = 300.0
gen_seed            = 173529



*** STK-14 Uppsala *** https://sites.google.com/site/stkmuu14/
Dr. Anik Sen,
Post Doctoral Fellow,
Ångströmlaboratoriet- Uppsala Universitet
Box 538
SE-751 21 Uppsala
Sweden
Phone no:- +46-722781705