<!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></FONT> </DIV>
<DIV><FONT face=Arial size=2>Thanks for response Mr.Alan Dodd</FONT></DIV>
<DIV><FONT face=Arial size=2>1) 1st run is simularion of position restrain of
protein in water (25000 steps) - system running very very slow
means for completion 10 steps it is taking more than 5 minutes or
more </FONT></DIV>
<DIV><FONT face=Arial size=2>2) 2nd simulation is production step of popc
in water (125000 steps ) - this is going normally means for completion 10
steps it is taking 3seconds or less than that. </FONT></DIV>
<DIV><FONT face=Arial size=2>i will send you the both input files of pr.mdp and
md.mdp files</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2><U>pr.mdp file ( This is already sent)
</U></FONT></DIV>
<DIV><FONT face=Arial
size=2>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</FONT></DIV>
<DIV><FONT face=Arial
size=2>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> </FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2><U>md.mdp file</U></FONT></DIV>
<DIV><FONT face=Arial size=2>cpp = /lib/cpp<BR>constraints =
all-bonds<BR>integrator = md<BR>dt = 0.002 ; ps !<BR>nsteps = 125000 ; total 250
ps.<BR>nstcomm = 1<BR>nstxout = 50<BR>nstvout = 10<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>Tcoupl = berendsen<BR>tc-grps = POPC
SOL<BR>tau_t = 0.1 0.1<BR>ref_t = 300 300<BR>; Energy monitoring</FONT></DIV>
<DIV><FONT face=Arial size=2>energygrps = POPC SOL<BR>; Isotropic pressure
coupling is now on<BR>Pcoupl = berendsen<BR>Pcoupltype = isotropic<BR>tau_p =
0.5<BR>compressibility = 4.5e-5<BR>ref_p = 1.0<BR>; Generate velocites is off at
300 K.<BR>gen_vel = no<BR>gen_temp = 300.0<BR>gen_seed = 173529</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2><BR><BR>pls anyone help me</FONT></DIV>
<DIV><FONT face=Arial size=2>thanks in advance.......</DIV></FONT></BODY></HTML>