[gmx-users] NPT simulation problems

[nicolas Dinter]

Dear Gromacs users,

I am trying to make a NPT MD simulation with 150 Benzenemethanethiol,
alfa-methyl molecules in a 30*30*30 box. After having found the equilibrium,
I run the NPT simulation and I had never found the box equilibrium, the size
is always decreasing, also after a 300 ps simulation!
Maybe the force field parameters are incorrect or the tau_p and tau_t are
not well choosen (parameters witch I don’t understand how to fit them).
If somebody could help me it will be very nice. Thank you.
See parameters files above.

Nicolas Dinter.

##mdp file for the mdrun##
title           = heating up MD 1
cpp             = /usr/bin/cpp
constraint      = all-bonds
integrator      = md
tinit           = 0.0
dt              = 0.002
nsteps          = 150000
nstcomm         = 1
nstxout         = 150
nstvout         = 0
nstfout         = 0
nstlist         = 10
ns_type         = simple
rlist           = 1.0
rcoulomb        = 1.0
rvdw            = 1.0
;box             = rectangular
; Temperature coupling is on in txo groups
Tcoupl          = berendsen
tc-grps         = nonp
tau_t           = 0.1
ref_t           = 293
; Pressure coupling is on
Pcoupl          = berendsen
pcoupltype      = isotropic
tau_p           = 1
compressibility = 4.5e-5
ref_p           = 1.0
; Generate velocites is on at 293 K
gen_vel         = no
gen_temp        = 293.0
gen_seed        = 173529

##top file##
;include forcefield parameters
#include "ffgmx.itp"

;include molecular topology file
#include "simple.itp"

[system]
nico

[molecules]
nico 150


##itp file##
; **************************** ;
; *** molecular topology   *** ;
; *** generated by pdb2itp *** ;
; **************************** ;

; *** original PDB header  *** :
; PROTEIN

[ moleculetype ]
;name    nrexcl
nico     3

; NUMBER OF ATOMS IN A MOLECULE =   10
; you need specify correct GROMACS atom types in type
; and charge group number (cgnr) and charge on atoms

[ atoms ]
;   nr    type       resnr  residu    atom    cgnr    charge
     1     CR61         1    NONP     C         1      0.0000
     2     CR61         1    NONP     C         1      0.0000
     3     CR61         1    NONP     C         1      0.0000
     4     CR61         1    NONP     C         1      0.0000
     5     CR61         1    NONP     C         1      0.0000
     6     CR61         1    NONP     C         1      0.0000
     7     CH1          1    NONP     C         1      0.0000
     8     S            1    NONP     S         1      0.0000
     9     CH3          1    NONP     C         1      0.0000
    10     HS           1    NONP     H         1      0.0000

; TOTAL CHARGE OF A MOLECULE    =    0.0000

; NUMBER OF BONDS IN A MOLECULE =   10
[ bonds ]
;   ai    aj funct           c0           c1
     2     1     1
     3     2     1
     4     3     1
     5     4     1
     6     1     1
     6     5     1
     7     1     1        0.13900        418400
     8     7     1        0.18300        376560
     9     7     1
    10     8     1

; NUMBER OF BENDS IN A MOLECULE =   12
[ angles ]
;   ai    aj    ak funct           c0           c1
     3     2     1     1
     4     3     2     1
     5     4     3     1
     6     1     2     1
     6     5     4     1
     5     6     1     1
     7     1     2     1          120.000      418.400
     7     1     6     1          120.000      418.400
     8     7     1     1          113.000      460.240
     9     7     1     1          120.000      418.400
     9     7     8     1          100.000      420.240
    10     8     7     1           96.000      397.480

; NUMBER OF TORSIONS IN A MOLECULE =   10
; check funct settings if your molecule has ring(s)

[ dihedrals ]
;   ai    aj    ak    al funct    phi0/q0     cp/cq   mult
     4     3     2     1     1    180.000     41.840   2
     5     4     3     2     1    180.000     41.840   2
     6     1     2     3     1    180.000     41.840   2
     6     5     4     3     1    180.000     41.840   2
     5     6     1     2     1    180.000     41.840   2
     1     6     5     4     1    180.000     41.840   2
     1     6     7     2     2
     8     7     1     2     1    180.000     41.840   2
     7     9     8     1     2      0.000    167.360
    10     8     7     1     1      0.000      2.929   3

; NUMBER OF 1-4 PAIR IN A MOLECULE =   11
[ pairs ]
;   ai    aj funct           c0           c1
     4     1     1
    10     1     1
     5     2     1
     8     2     1
     9     2     1
     6     3     1
     7     3     1
     7     5     1
     8     6     1
     9     6     1
    10     9     1

; this is the last line and shows successful generation