[gmx-users] cg warning

[Nuno R. L. Ferreira]

On Tuesday 08 June 2004 06:02 pm, Derrick Guang Yuh Lee wrote:
> dear nuno
>
> when i run a energy minimization w/ "integrator = cg" and "constraints =
> none", i get "potential energy = nan".
>
> but when i run it with "integrator = steep" first, and then cg (all with
> contraints = none), it'll work fine. unfortunately, when i run that with
> "contraints = all-bonds", i get the original error about cg not
> implemented, again. i'm thinking it's probably my em.mdp file, which is
> this:
>
> title 		= energy minimization
> cpp 		= /lib/cpp
> define 		= -DFLEX_SPC
> constraints 	= all-bonds
> integrator 	= cg
> nsteps 		= 500000
> ;
> ;  Energy minimizing stuff
> ;
> emtol 		= 5000
> emstep 		= 0.01
> nstcgsteep	= 5000
>
> nstlist		= 10
> ns_type		= grid
> rlist		= 0.9
> rcoulomb	= 0.9
> rvdw		= 1.4
> Tcoupl		= no
> Pcoupl		= no
> gen_vel		= no
>
> if you can tell me what could be going horrible wrong, it'd be very much
> appreciated.
>

So you are using coulombtype = Cut-off (default, when not specified in the mdp 
file).  You should use rcoulomb > than rlist, like rcoulomb=1.8

Regards,
Nuno

P.S. Or try the new l-bfgs algorithm.  I also have a lipid system, and it 
works.



>
>  - derrick
>
> > On Monday 07 June 2004 04:39 pm, Derrick Guang Yuh Lee wrote:
> > > dear gmx-users
> > >
> > > i attempted to run an energy minimization with integrator = cg and
> > > constraints = all-bonds, and i keep getting the following error:
> > >
> > > ---------------------------------------------------------------
> > > Warning: as of GMX v 2.0 unit of compressibility is truly 1/bar
> > > checking input for internal consistency...
> > > ERROR: constraints with Conjugate Gradients not implemented
> > > Generated 1174 of the 2016 non-bonded parameter combinations
> > > Excluding 3 bonded neighbours for DPPC 40
> > > Excluding 2 bonded neighbours for SOL   1448
> > > processing coordinates...
> > > double-checking input for internal consistency...
> > > ERROR: can not do Conjugate Gradients with constraints (4856)
> > > Fatal error: There were 2 errors
> > > ---------------------------------------------------------------
> > >
> > > and was curious what does this mean and how can i deal with it?
> >
> > Have you tryed cg + constraints = none ?
> >
> > > additionally, could someone explain to me in a little detail the
> > > significant difference between setting constraints between none and
> > > all-bonds?
> >
> > The constraints are used to maintain some properties, like bond lenghts
> > and angles, within a meaningfull interval, defined in the f.f.
> > Check the manual, chapter 3.6
> >
> >
> >
> >  i've been assuming that with all-bonds, the water molecules
> >
> > > angles are constraint such that the angle between the H bonds are the
> > > same. thank you in advance.
> > >
> > >
> > >  - derrick
> > >
> > >
> > >  derrick Lee
> > >  faculty of Science
> > >  Memorial University of Newfoundland
> > >  k24dgyl at mun.ca / derrickglee at hotmail.com
> > >
> > > "a teacher is never a giver of truth - he is a guide, a pointer to the
> > > truth that each student must find for himself. a good teacher is merely
> > > a catalyst."
> > >                                                               - bruce
> > > lee
> > >
> > >
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> > --
> > **********************************************
> > Nuno Ricardo Santos Loureiro da Silva Ferreira
> > Grupo de Química Biológica
> > Departamento Química
> > Universidade de Coimbra
> > Portugal
> > www.biolchem.qui.uc.pt
> > **********************************************
> > "Do not worry about your difficulties in maths.
> >  I can assure you that mine are still greater."
> >                                    emc2
> >
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-- 
**********************************************
Nuno Ricardo Santos Loureiro da Silva Ferreira
Grupo de Química Biológica 
Departamento Química
Universidade de Coimbra
Portugal
www.biolchem.qui.uc.pt
**********************************************
"Do not worry about your difficulties in maths.
 I can assure you that mine are still greater."
                                   emc2