[gmx-users] pme + barostat

[Valentin Gogonea]

Dear gromacs users,

I am trying to run a short simulation of a small organic molecule in 
water. When I use PME with Parrinello-Rahman barostat the density 
changes dramatically and wholes appear in the simulation box. This 
doesn't happen when I replace PME with cutoff.

Did anybody experience this problem and how can I get it fixed?

Thank you for your help.

Valentin

title               =  ${MOL} ;MD
cpp                 =  /usr/bin/cpp
constraints         =  all-bonds
integrator          =  md
dt                  =  0.002	; ps !
nsteps              =  5000	; total 5 ps.
nstcomm             =  1
nstxout             =  100
nstvout             =  0
nstfout             =  0
nstlist             =  10
ns_type             =  grid
rlist               =  0.5
rcoulomb            =  0.5
rvdw                =  0.5
pbc                 = xyz
coulombtype         = pme
; Berendsen temperature coupling is on in 2 groups
Tcoupl              =  nose-hoover
tau_t               =  0.1
tc-grps		        =  system
ref_t               =  300
; Pressure coupling is not on
Pcoupl              =  Parrinello-Rahman
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