[gmx-users] Melittin in methanol...

[sharada]

Dear Justin,
Even with the new force field I am getting the same result. 
My 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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