[gmx-users] position restraints

[Dmitry Kovalsky]

Hi there,

I have some troubles with position restraints simulation.

 When I run the pr simulation at 310K with our without pressure coupling ( 
this doesn't matter) for a 50 ps it ALWAYS crashes near 20-30 ps,  writes 
that distance more then 4.41 and so on. Reducing time step doesn't help.

here is my mdp file 
cpp                 =  /lib/cpp
define              =  -DPOSRES
constraints         =  none
integrator          =  md
dt                  =  0.002
nsteps              =  25000
nstxout             =  500
nstxtcout           =  500
nstvout             =  500
nstfout             =  500
nstlog              =  500
nstcomm             =  1
coulombtype         =  PME
rcoulomb            =  0.9
rcoulomb_switch     =  0
pme_order           =  4
optimize_fft        =  yes
fourierspacing      =  0.12
ns_type             =  grid
vdwtype             =  Cut-off
rlist               =  0.9
rvdw                =  1.5
nstlist             =  10
; Generate velocites is on at 300 K.
gen_vel             =  yes
gen_temp            =  310.0
gen_seed            =  2151736
; Berendsen temperature coupling is on in two groups
Tcoupl              =  berendsen
tau_t               =  0.1	
tc_grps		=  system
ref_t               =  310   
; Pressure coupling is not on
Pcoupl              =  no   ; or berendsen
;tau_p               =  0.5
compressibility     =  4.5e-5
ref_p               =  1.0

The other problem is with parallel runs

If I run a pr simualtion at one processor it runs ok, but when I use parallel 
it crashes  rapidly. Does parallel play a role in a simulation results?

I would appreciate for any help

Dima
 
-- 
Sincerely yours,

Ph.D. Student Dmitry Kovalsky
Institute of Molecular Biology & Genetics
150 Akad. Zabolotnogo Street,
Kiev-143, 03143
UKRAINE

E-mail: dikov at imbg.org.ua
Fax:  +380 (44) 266-0759
Tel.: +380 (44) 266-5589