<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<HTML><HEAD>
<META http-equiv=Content-Type content="text/html; charset=iso-8859-1">
<META content="MSHTML 6.00.2900.3243" name=GENERATOR>
<STYLE></STYLE>
</HEAD>
<BODY bgColor=#ffffff>
<DIV><FONT face=Arial size=2>hi gromacs users, </FONT></DIV>
<DIV><FONT face=Arial size=2>iam getting problem while doing postion
restrian for the protein system reunning very slow, </FONT></DIV>
<DIV><FONT face=Arial size=2>but i have done md.mdp for another system(
bilayer-popc) its running normally, </FONT></DIV>
<DIV><FONT face=Arial size=2>whats the problem in my protein
system?</FONT></DIV>
<DIV><FONT face=Arial size=2>i have used pr.mdp file like i am enlosing
along with my mail</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2> User spoel
(236)<BR>; Wed Nov 3 17:12:44
1993<BR>; Input
file<BR>;<BR>title
=
Yo<BR>cpp
=
/usr/bin/cpp<BR>define
= -DPOSRES<BR>constraints
=
all-bonds<BR>integrator
=
md<BR>dt
=
0.002<BR>nsteps
=
25000<BR>nstcomm
=
1<BR>nstxout
=
50<BR>nstvout
=
1000<BR>nstfout
=
0<BR>nstlog
=
10<BR>nstenergy
=
10<BR>nstlist
=
10<BR>ns_type
=
grid<BR>rlist
=
1.0<BR>rcoulomb
=
1.0<BR>rvdw
=
1.0<BR> pbc
= xyz<BR>; Berendsen temperature coupling is on in two groups<BR>;
Pressure coupling is
on<BR>Tcoupl
=
berendsen<BR>tc-grps
= Protein SOL
Na+<BR>tau_t
= 0.1 0.1
0.1<BR>ref_t
= 300 300
300<BR>Pcoupl
=
parrinello-rahman<BR>pcoupltype
=
isotropic<BR>ref_p
=
1<BR>tau_p
= 0.5<BR>compressibility = 4.5e-5<BR>;
Energy
monitoring<BR>energygrps
= Protein SOL Na+<BR>; Generate velocites is on at 300
K.<BR>gen_vel
=
yes<BR>gen_temp
=
300.0<BR>gen_seed
=
173529<BR>
41,1
Bot<BR>
3,1 Top<BR>pls help
me in this problem</FONT></DIV></BODY></HTML>