[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
#ifdef FLEX_SPC
#include "flexspc.itp"
#include "spc.itp"

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 ]


> Thanks
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