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.war...@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-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of sarbani chattopadhyay Sent: Friday, 26 February 2010 12:06 AM To: gmx-users@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" command. 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 Sarbani. <http://sigads.rediff.com/RealMedia/ads/click_nx.ads/www.rediffmail.com/signatureline....@middle?>
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