[gmx-users] NM and minimisation problems
Nguyen Hoang Phuong
phuong at theochem.uni-frankfurt.de
Wed Feb 11 12:43:00 CET 2004
> I try to do a normal mode analysis of a molecule. What interest me is just a part I suppose to be a hinge.
> It is my first try so don't hit me too hard...
> My first problem is minimization.
> MDRUN output tell me energy is still high for a nm run
> Maximum force: 3.76287e+04
> So I want to minimise, using GROMACS CG. I have searched the manuals and the user archive and see that i have to remove all constraints. That's what I am trying to do now, but I still obtain
> ERROR: constraints with Conjugate Gradients not implemented
> ERROR: can not do Conjugate Gradients with constraints (3217)
> what are the settings I have to disable in the .mdp file to run it smoothly?
first, you should have a look at the top file, if you see something like
; Include water topology
then you can try with this file:
title = xxxx
cpp = /lib/cpp
include = -I../top
define = -DFLEX_SPC
integrator = cg
emtol = 0.000001
emstep = 0.000001
nstcgsteep = 100
nsteps = 50000
nstxout = 50
xtc_grps = Protein
energygrps = Protein
nstlist = 5
ns_type = grid
rlist = 1.
vdwtype = cut-off
coulombtype = PME
rcoulomb = 1.
rvdw = 1.
and also make sure that in your top file, you should not have the line
[ constraints ]
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