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.<br />
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