On 9/19/13 11:59 AM, fatemeh ramezani wrote:
Dear Justin
I used gromacs OPLSAA forcefield for simulation of protein and TIP3P model for
water.
em.mdp file:
title = n.pdb
cpp = /lib/cpp
define = -DFLEXIBLE
constraints = none
integrator = steep
nsteps = 4
constraint_algorithm =
shake_tol = 0.0001
nstenergy = 10
nstxtcout = 1
nstlist = 5
nstcomm = 1
ns_type = grid
rlist = 1
coulombtype = PME
rcoulomb= 1
rvdw= 1
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 8
ewald_rtol = 1e-5
optimize_fft= yes
emtol = 1000.0
emstep = 0.01
md.mdp file:
title = n.pdb restraining
cpp = /lib/cpp
constraints = none
integrator = md
dt = 0.0008
nsteps = 2500
nstcomm = 10
comm_mode =
nstxout = 250
nstvout = 1000
nstfout = 0
nstlog = 10
nstenergy = 10
nstlist = 10
ns_type = grid
rlist = 0.9
coulombtype = PME
rcoulomb= 0.9
rcoulomb-switch = 1
rvdw= 0.5
vdwtype = shift
Your van der Waals settings make no sense. I strongly suspect that this is
inducing very nasty artifacts.
-Justin
;rvdw-switch = 0.6
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 6
ewald_rtol = 1e-5
optimize_fft= yes
; Berendsen temperature coupling is on in three groups
Tcoupl = V-rescale
tau_t = 0.1 0.1
tc-grps= Protein Non-Protein
ref_t = 300 300
; Pressure coupling is on
;Pcoupl = berendsen
Pcoupl = no
Pcoupltype = isotropic
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
energygrps = Protein Sol
Fatemeh Ramezani
--
==
Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
==
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
