[gmx-users] Energy minimization

Andrea Bacconi andreab at physiol.unizh.ch
Wed Jan 12 18:48:00 CET 2005

Hi All,
I'm continuing my MD simulation in water, everything is ok up to the 
energy minimization step. I think I understood the problem but I don't 
know how to solve it.
When I run EM in void all is ok Fmax is around 25 but when I add water 
I'm not able to minimize the system's energy (only Fmax >>1000) using 
steep descent alghorithm.
Now, when I use cg, instead I get this error message from grompp : 
ERROR: can not do Conjugate Gradients with constraints (59565)
My em.mdp file is the following.

cpp                      = /lib/cpp
constraints            =none
define                  = -DFLEX_SPC
integrator             = cg
dt                        = 0.002
nsteps                  = 100000
nslist                    = 10
ns_type               = grid
rlist                      = 0.9
coulombtype        = PME
rcoulomb              = 1.8
rvdw                     = 0.9

nstcgsteep            = 100
emtol                    = 1000.0
emstep                  = 0.001

I looked up in the mailing list for a similar problem, I found it but it 
was not usefull. To my mind it looks like that the program sees some 
consraints when water is around because when I simulate the same protein 
in void everything is fine sd and cg (no problem at all).
So please help me if you can
thank you for your attention

More information about the gromacs.org_gmx-users mailing list