[gmx-users] energy minimization problem
sarbani_c84 at rediffmail.com
Thu Feb 25 14:05:56 CET 2010
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...
More information about the gromacs.org_gmx-users