[gmx-users] Energy minimization
andreab at physiol.unizh.ch
Wed Jan 12 18:48:00 CET 2005
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
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
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