[gmx-users] Energy minimization

[David]

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
try
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.


> Andrea
> 
> 
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
-- 
David.
________________________________________________________________________
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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++