[gmx-users] energy minimization problem

Dallas B. Warren Dallas.Warren at pharm.monash.edu.au
Fri Feb 26 00:43:54 CET 2010

Actual text input / output would be a good idea here.  What is the actual output when you try to run it the second time?


Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at pharm.monash.edu.au
+61 3 9903 9167
When the only tool you own is a hammer, every problem begins to resemble a nail. 


From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of sarbani chattopadhyay
Sent: Friday, 26 February 2010 12:06 AM
To: gmx-users at gromacs.org
Subject: [gmx-users] energy minimization problem


Hi ,
I have a protein with 2 chains. I need to do normal mode analysis on it. As there are no 
covalent bonds between the two chains, I did not use the "merge" option in the "pdb2gmx" 
I am trying to energy minimize the structure , in vaccum.( in double precision) , but am not 
able to get the Fmax below e-02. i have tried using the "l-bgs" minimization technique. 
The lbfgs.mdp file is as follows
define = -DFLEXIBLE
constraints = none
integrator = l-bfgs
tinit = 0
nsteps = 10000
nbfgscorr = 10
emtol = .001
emstep = 0.5
gen_vel = no
gen-temp = 300
nstcomm = 1
ns_type = grid
rlist = 1.2
rcoulomb = 1.2
rvdw = 1.0
Tcoupl = no
Pcoupl = no
coulombtype = PME
vdwtype = shift

The minimization continues up to the specified no. of steps. When I try to give another 
minimization run on the minimized structure, the Fmax goes upto the order "e+00".

I am not being able to figure out the problem. 
Any suggestion regarding this will be very helpful. 
Thanks in advance



-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100226/628114a2/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: ~WRD000.jpg
Type: image/jpeg
Size: 823 bytes
Desc: ~WRD000.jpg
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100226/628114a2/attachment.jpg>

More information about the gromacs.org_gmx-users mailing list