[gmx-users] cg warning

[Derrick Guang Yuh Lee]

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.


 - 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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