[gmx-users] Is something wrong wih my mdp?
chenxianli
1471769256 at qq.com
Tue Apr 8 05:47:30 CEST 2014
Hi all!
Recently I have been doing the MD simulation about the ratio of opening
and closing of RNA base pais in different Na ion concentrations. Runing 20
ns simulation using Gromacs.
As far as I know,in most articles on this problem saying: the higher Na ion
concentration ,the more stable of RNA structure,so the probility of base
pair opening will decrease .But I can't get the same results... Does anyone
konw why ?
After runing equilibrium, my mdp file is as follows:
title = 1ZIH
define = -DPOSRES
cpp = /lib/cpp
constraints = all-bonds
;run parameters
integrator = md
dt = 0.002 ; ps
nsteps = 1000000 ; total 0.2ns
nstcomm = 100
;output control
nstxout = 1000 ; collect data every 2 ps
nstxtcout = 1000
nstvout = 1000
nstfout = 0
nstlog = 1000
nstcalcenergy = 100 ;frequency fo calculating the
energy
nstenergy = 1000 ;frequency to write energies
to energy file
;Bond parameter
continuation = no ;no constant restarting
constraint-algorithm = lincs
lincs_iter = 1
lincs_order = 4
;Neighborsearching
ns_type = grid
nstlist = 5
rlist = 1.0
rcoulomb = 1.0
vdwtype = cut-off
rvdw = 1.0
;Electrostatics
coulombtype = PME
pme_order = 4
fourierspacing = 0.12
;Temperature coupling is on
Tcoupl = V-rescale ;berendsen
tc-grps = RNA SOL NA CL
Tau_t = 0.1 0.1 0.1 0.1
ref_t = 350 350 350 350
; Berendsen Pressure coupling is on
Pcoupl = Parrinello-Rahman
refcoord-scaling = all
Pcoupltype = isotropic
tau_p = 0.5
compressibility = 4.5e-05
ref_p = 1.0
;Periodic boundary conditions
pbc = xyz
;Dispersion correction
DispCorr = EnerPres
; Generate velocites is on at 300 450 500 550 K.
gen_vel = yes
gen_temp = 350
gen_seed = 173529
Is something wrong with my mdp file?
Thanks !
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