[gmx-users] Energy minimization
spoel at xray.bmc.uu.se
Wed Jan 12 18:57:34 CET 2005
On Wed, 2005-01-12 at 18:48 +0100, Andrea Bacconi wrote:
> 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
define = -DFLEXIBLE
although it should work.
> integrator = cg
> dt = 0.002
> nsteps = 100000
> nslist = 10
> ns_type = grid
> rlist = 0.9
> coulombtype = PME
> rcoulomb = 1.8
This means you are combining a twin-range Coulomb potential with PME.
That is weird. You can set rcoulomb=0.9, rvdw might be somewhat bigger
depending on the force field.
> 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
Do also check the tpr file
gmxcheck -s topol.tpr | more
and search for CONS (constraints). You shouldn't have any.
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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