<HTML>
<HEAD>
<META content="text/html; charset=big5" http-equiv=Content-Type>
<META content="OPENWEBMAIL" name=GENERATOR>
</HEAD>
<BODY bgColor=#ffffff>
<font size="2"><font face="Arial, Helvetica">Sorry for the abnormal code.
<br />
I have fixed
that.
<br />
---
<br />
Hi,
<br />
<br />
My gromacs version is 4.0.5.
<br />
I used grompp to generate tpr for 1ps simulation in this way
<br />
grompp -f md1.mdp -n index.ndx  -p topol.top -c 0ps.gro  -t 0ps.trr -o
1ps.tpr
<br />
mdrun -s 1ps.tpr -e 1ps.edr -o 1ps.trr -g 1ps.log -c 1ps.gro
<br />
Here is my md1.mdp file:
<br />
</font><font face="Arial, Helvetica">;
<br />title = ttt
<br />cpp = /lib/cpp  
<br />constraints = hbons
<br />;define = -DFLEX_SPC  
<br />integrator = md 
<br />emtol = 100.0
<br />emstep = 0.005 
<br />dt = 0.002 ; ps!
<br />nsteps = 500 ; total 1ps
<br />nstcomm = 500  
<br />ntsxout = 500  
<br />ntsvout = 500 
<br />ntsfout = 500  
<br />ntslog = 500 
<br />nstenergy = 500
<br />nstlist = 5   
<br />ns_type = grid  
<br />
rlist = 1.
<br />
rcoulomb = 1.
<br />
rvdw = 1.
<br />
coulombtype = PME
<br />
fourierspacing = 0.12
<br />
pme_order = 4
<br />
optimize_fft = yes
<br />
Tcoupl = v-rescale
<br />
rc-grps = A-chain B-chain drug SOL NA+
<br />
;tau_t = 0.1 0.1
<br />
tau_t =0.2 0.2 0.2 0.2
<br />
ref_t = 300.000000 300.000000 300.000000 300.00000 300.000000
<br />
energygrps = A-chain B-chain druhg SOL NA+
<br />
Pcoupl = berendsen
<br />
Pcoupltype = isotropic
<br />;tau_p = 0.1
<br />
tau_p = 0.25
<br />
compressibility = 5.4e-5
<br />
ref_p = 1.0
<br />gen_vel = yes
<br />gen_temp = 300.000000
<br />gen_seed = 173531
<br />
gen_seed           
=  173531 </font><font face="Arial,
Helvetica">
<br />
----------------------------------------------
<br />
Then I execute below loop in other 59999 times for the totaly 60ns trajectories.
<br />
grompp -f md2.mdp -n index.ndx  -p topol.top -c ${n-1}ps.gro  -t
${n-1}ps.trr -o ${n}ps.tpr
<br />
mdrun -s ${n}ps.tpr -e ${n}ps.edr -o ${n}ps.trr -g ${n}ps.log -c ${n}ps.gro
<br />
The file md2.mdp is almost the same as md1.mdp but the parameter gen_vel=no.
<br />
Here ${n-1}ps.gro and ${n-1}.trr mean I use last time frame trajectory
to continue.(I didn't really use this commend $(n-1) in bash script, it
won't work.)
<br />
<br />
I change the other way to run parallel simulation on the same system
for
double check since above script is difficult to parallelize in public
computer.
<br />
The new method is:
<br />
grompp -f md60ns.mdp -n index.ndx  -p topol.top -c 0ps.gro  -t 0ps.trr
-o 60ns.tpr
<br />
mpiexec -np 8 mdrun_mpi -s 60ns.tpr -e 60ns.edr -o 60ns.trr -g 60ns.log -c
60ns.gro
<br />
The only different between md1.mdp and md60ns.mdp is nstep=30000000 in
md60ns.mdp.
<br />
<br />
Theses two data generated by different ways are totaly different.
<br />
Here I mean different is not on the number buy mean the tendency of figure.
<br />
In the movie of first method, protein runs violently and go outside the periodic
boundary and then split by cubic edge.
<br />
The interaction energy within protein also fluctuate in an unstable way.
<br />
<br />
On the contrary, the second method generate a stable movie and fluctuation of
interaction energy.
<br />
Theotically these two should be the same, right?
<br />
Is anything wrong in my work?
<br />
<br />
Sincerely yours,
<br />
Hsin-Lin
</font>
<br /><b>------- End of Forwarded Message
-------</b>
<br />
<br />
<br />
</font>
</BODY>
</HTML>