[gmx-users] water dimer is gas phase

[Nilesh Dhumal]

Hello,

I am trying a simulation for water dimer in vaccum (gas phase).
Here I run the simulation with following steps

This is the .pdb file before energy minimization

TITLE     S  C  A  M  O  R  G
REMARK    THIS IS A SIMULATION BOX
CRYST1    3.000    3.000    3.000  90.00  90.00  90.00 P 1           1
MODEL        1
ATOM      1  OW  WAT     1       0.317   1.494   1.565  1.00  0.00
ATOM      2  HW1 WAT     1      -0.091   2.293   1.258  1.00  0.00
ATOM      3  HW2 WAT     1      -0.144   0.788   1.129  1.00  0.00
ATOM      4  OW  WAT     2       3.172   1.515   1.356  1.00  0.00
ATOM      5  HW1 WAT     2       2.224   1.482   1.459  1.00  0.00
ATOM      6  HW2 WAT     2       3.522   1.427   2.231  1.00  0.00
TER
ENDMDL

I run the energy minimization

grompp -f minim-gas.mdp  -c dimer.pdb -p dimer.top -o dimer.tpr

mdrun -pd   -s dimer.tpr -o dimer.trr -c dimer.pdb -e dimer.edr -g dimer.log

I got the following file which I could visualize


TITLE     Protein
MODEL        1
ATOM      1  OW  WAT     1       0.351   1.490   1.592  1.00  0.00
ATOM      2  HW1 WAT     1      -0.106   2.335   1.248  1.00  0.00
ATOM      3  HW2 WAT     1      -0.162   0.750   1.112  1.00  0.00
ATOM      4  OW  WAT     2       3.198   1.519   1.321  1.00  0.00
ATOM      5  HW1 WAT     2       2.174   1.481   1.457  1.00  0.00
ATOM      6  HW2 WAT     2       3.544   1.423   2.268  1.00  0.00
TER
ENDMDL

minim-gas.mdp file

title               =  cpeptide
cpp                 = /usr/bin/cpp
constraints         = none
integrator          = steep
dt                  =  0.002    ; ps !
nsteps              =  50000
nstlist             =  1
coulombtype         = cut-off
vdwtype             = cut-off
ns_type             =  simple
rlist               =  0.0
rcoulomb            =  0.0
rvdw                =  0.0
fourierspacing      = 0.12
fourier_nx               = 0
fourier_ny               = 0
fourier_nz               = 0
pme_order           = 4
ewald_rtol          = 1e-5
optimize_fft        = yes
pbc                 = no
;       Energy minimizing stuff
;
emtol               =  1000.0
emstep              =  0.01

the I run equlibration

grompp -f minim-pr.mdp  -c dimer.pdb -p dimer.top -o dimer.tpr

mdrun -pd   -s dimer.tpr -o dimer.trr -c dimer.pdb -e dimer.edr -g dimer.log

I got the following file which I could not visualize


TITLE     Protein
MODEL        1
ATOM      1  OW  WAT     1    -2737.208 974.242-2091.510  1.00  0.00
ATOM      2  HW1 WAT     1    -2737.949 973.910-2090.885  1.00  0.00
ATOM      3  HW2 WAT     1    -2736.363 974.004-2091.048  1.00  0.00
ATOM      4  OW  WAT     2    2740.655-971.0932094.500  1.00  0.00
ATOM      5  HW1 WAT     2    2740.852-971.7332093.873  1.00  0.00
ATOM      6  HW2 WAT     2    2740.420-971.4722095.431  1.00  0.00
TER
ENDMDL

the equlibration file I used

title               =  cpeptid position restraining
cpp                 =  /usr/bin/cpp
constraints         =  none
integrator          =  md
dt                  =  0.001    ; ps !
nsteps              =  1000000      ; total 1.0 ps.
nstcomm             =  1
nstxout             =  10000
nstvout             =  10000
nstfout             =  0
nstlog              =  10
nstenergy           =  10
nstlist             =  10
ns_type             =  simple
comm_mode           = none
coulombtype         = cut-off
vdwtype             = cut-off
rlist               =  0.0
rcoulomb            =  0.0
rvdw                =  0.0
pbc                 =  no
fourierspacing      = 0.12
fourier_nx               = 0
fourier_ny               = 0
fourier_nz               = 0
pme_order           = 4
ewald_rtol          = 1e-5
optimize_fft        = yes
; Berendsen temperature coupling is on
Tcoupl = nose-hoover
tau_t = 0.1
tc-grps  =system
ref_t =   298
; Pressure coupling is  on
Pcoupl              = NO ;Parrinello-Rahman
pcoupltype          = isotropic
tau_p               =  2.0
compressibility     =  4.5e-5
ref_p               =  1.0
; Generate velocites is on at 300 K.
gen_vel             =  yes
gen_temp            =  298.0
gen_seed            =  173529

Is ther any thing wrong with my mdp files.
WHy they is so much change is cooridnates in the .pdb file.

I am using gromacs version 4.0.7.

Thanks

Nilesh