[gmx-users] energy minimization problem

sarbani chattopadhyay sarbani_c84 at rediffmail.com
Thu Feb 25 14:05:56 CET 2010

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
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