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<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Actual text input / output would be a good idea here. What is
the actual output when you try to run it the second time?<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Catch ya,<br>
<br>
Dr. Dallas Warren<br>
</span><span style='font-size:10.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Drug Delivery, Disposition and Dynamics</span><span
style='font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><br>
</span><span style='font-size:10.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Monash Institute of Pharmaceutical Sciences</span><span
style='font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>,
Monash University<br>
381 Royal Parade, Parkville VIC 3010<br>
dallas.warren@pharm.monash.edu.au<br>
+61 3 9903 9167<br>
---------------------------------<br>
When the only tool you own is a hammer, every problem begins to resemble a
nail.</span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'> <o:p></o:p></span></p>
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<p class=MsoNormal><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span
style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> gmx-users-bounces@gromacs.org
[mailto:gmx-users-bounces@gromacs.org] <b>On Behalf Of </b>sarbani
chattopadhyay<br>
<b>Sent:</b> Friday, 26 February 2010 12:06 AM<br>
<b>To:</b> gmx-users@gromacs.org<br>
<b>Subject:</b> [gmx-users] energy minimization problem<o:p></o:p></span></p>
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<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal style='margin-bottom:12.0pt'>Hi ,<br>
I have a protein with 2 chains. I need to do normal mode analysis on it. As
there are no <br>
covalent bonds between the two chains, I did not use the "merge"
option in the "pdb2gmx" <br>
command. <br>
I am trying to energy minimize the structure , in vaccum.( in double precision)
, but am not <br>
able to get the Fmax below e-02. i have tried using the "l-bgs"
minimization technique. <br>
The lbfgs.mdp file is as follows<br>
define = -DFLEXIBLE<br>
constraints = none<br>
integrator = l-bfgs<br>
tinit = 0<br>
nsteps = 10000<br>
nbfgscorr = 10<br>
emtol = .001<br>
emstep = 0.5<br>
gen_vel = no<br>
gen-temp = 300<br>
nstcomm = 1<br>
ns_type = grid<br>
rlist = 1.2<br>
rcoulomb = 1.2<br>
rvdw = 1.0<br>
Tcoupl = no<br>
Pcoupl = no<br>
coulombtype = PME<br>
vdwtype = shift<br>
<br>
The minimization continues up to the specified no. of steps. When I try to give
another <br>
minimization run on the minimized structure, the Fmax goes upto the order
"e+00".<br>
<br>
I am not being able to figure out the problem. <br>
Any suggestion regarding this will be very helpful. <br>
Thanks in advance<br>
Sarbani.<o:p></o:p></p>
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