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.
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
