[gmx-users] Melittin in methanol...

[sharada]

Dear Justin,
Even with the new force field I am getting the same result. 
The  methanol. gro file , em.mdp, pr,mdp and md.mdp files looks like these
Methanol, 1 bar, 300K, equilibrated using PME, BdG 21-09-2001
648
1MeOH Me1 1 1.970 1.460 1.209 -0.8587 -0.1344 -0.0643
1MeOH O2 2 1.978 1.415 1.082 0.0623 -0.1787 0.0036
1MeOH H3 3 1.905 1.460 1.030 -0.5020 -0.9564 0.0997
2MeOH Me1 4 2.013 0.181 0.123 0.0317 0.4268 -0.0034
2MeOH O2 5 1.980 0.097 0.224 -0.8424 -0.0021 -0.6308
2MeOH H3 6 2.060 0.100 0.284 -0.7967 -0.7548 -0.6455
3MeOH Me1 7 2.008 0.409 0.498 -0.6920 0.4374 0.2455
3MeOH O2 8 2.109 0.460 0.422 -0.6105 0.1049 0.1322
3MeOH H3 9 2.170 0.506 0.486 -0.6959 -1.9809 1.8452
4MeOH Me1 10 1.856 1.779 1.151 -0.2574 0.2271 -0.0352
4MeOH O2 11 1.951 1.877 1.153 0.0214 -0.0482 0.2841
EM.mdp....
; VARIOUS PREPROCESSING OPTIONS = 
title = mellitin
cpp = /lib/cpp
define = -DFLEXIBLE
; RUN CONTROL PARAMETERS = 
integrator = steep
; start time and timestep in ps = 
tinit = 0
dt = 0.001
nsteps = 4000
nstlist =10
ns_type =grid
rlist =0.5
rcoulomb =1.4
vdwtype =cutoff
rvdw =0.8
; ENERGY MINIMIZATION OPTIONS = 
emtol = 0.00001
emstep = 0.1
nstcgsteep = 1000
PR.mdp.....
warnings = 10
cpp = /lib/cpp
define = -DPOSRES
constraints = all-bonds
integrator = md
dt = 0.002 ; ps !
nsteps = 1000 ; total 1.0 ps.
nstcomm = 1
nstxout = 10
nstvout = 1000
nstfout = 0
nstlog = 10
nstenergy = 10
nstlist = 10
ns_type = grid
rlist = 0.5
rcoulomb = 1.4
rvdw = 0.8
epsilon_r = 66
; Berendsen temperature coupling is on in two groups
Tcoupl = nose-hoover
tau_t = 0.1 0.1
tc-grps = Protein other
ref_t = 300 300 
; 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
MD.mdp...
cpp = /lib/cpp
constraints = all-bonds
integrator = md
tinit = 100
dt = 0.002 ; ps !leapfrog algorithm 2fs timestep
nsteps = 1000000 ; total 2 ns.
nstcomm = 1
nstxout = 10000
nstvout = 5000
nstfout = 0
nstlist = 10
ns_type = grid
rlist = 0.5
rcoulomb = 1.4
rvdw = 0.8
epsilon_r = 66.0
; Berendsen temperature coupling is on in two groups
Tcoupl = Berendsen
tau_t = 0.1 0.02
tc-grps = protein other
ref_t = 300 300
solvent_optimization = sol
; Energy monitoring
energygrps = Protein other
; Pressure coupling is not on
Pcoupl = Berendsen
tau_p = 2.0
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
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I have mailed the itp for methanol that I am using in my previous mail. Kindly give me advice as to why I am getting similar results for water and methanol.
Thanks..
sharada
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