[gmx-users] problem in pr.mdp file

[Alan Dodd]

What's the difference between the two runs?  Isolate which of the differences makes your simulation run slow, and then the answer might present itself.


----- Original Message ----
From: sudheer <sudheer.pbm07 at gmail.com>
To: gmx-users at gromacs.org
Sent: Monday, December 31, 2007 12:20:48 PM
Subject: [gmx-users] problem in pr.mdp file


hi gromacs users, 
iam getting problem while doing postion restrian for the protein system reunning very slow, 
but i have done md.mdp for another system( bilayer-popc) its running normally, 
whats the problem in my protein system?
i have used pr.mdp file like i am enlosing along with my mail
 
  User spoel (236)
;       Wed Nov  3 17:12:44 1993
;       Input file
;
title               =  Yo
cpp                 =  /usr/bin/cpp
define              =  -DPOSRES
constraints         =  all-bonds
integrator          =  md
dt                  =  0.002
nsteps              =  25000
nstcomm             =  1
nstxout             =  50
nstvout             =  1000
nstfout             =  0
nstlog              =  10
nstenergy           =  10
nstlist             =  10
ns_type             =  grid
rlist               =  1.0
rcoulomb            =  1.0
rvdw                =  1.0
  pbc                 =  xyz
; Berendsen temperature coupling is on in two groups
; Pressure coupling is on
Tcoupl              =  berendsen
tc-grps             =  Protein   SOL    Na+
tau_t               =  0.1       0.1    0.1
ref_t               =  300       300    300
Pcoupl              =  parrinello-rahman
pcoupltype          =  isotropic
ref_p               =  1
tau_p               =  0.5
compressibility     =  4.5e-5
; Energy monitoring
energygrps          =  Protein  SOL  Na+
; Generate velocites is on at 300 K.
gen_vel             =  yes
gen_temp            =  300.0
gen_seed            =  173529
                                                              41,1          Bot
                                                            3,1           Top
pls help me in this problem


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