Re: Minimization

From: Luca (bellucci14_at_unisi.it)
Date: Wed May 23 2007 - 02:42:31 CDT

On Tuesday 22 May 2007 17:47, Rita Cassia wrote:
Hi Rita,
cutoff 10 and pairlistdist of 12 o 14
are very standard and good choice if you use PBC with PME.
Many people , with large system, use cutoff=8.0. See article in pubblication
list of NAMD site.
Cutoff of 23 and pairlistdist 25 angstrom for direct potential is very large.
With this value the times of simulation are much long.

Ciao
Luca

> Hi Luca,
>
> thanks for your email and I had made those changes and the minimization has
> worked out.
>
> Can I ask you something? Also for huge complexes, in solvent boxes, the
> standard values for the cutoff and pairlistdist are still recommended or do
> I have to increase them?
>
> I have done simulations with pheo complexes in water, 8 Chromophores, and I
> had chosen a cutoff of 23. The simulation had worked but I am not sure, if
> it was necessary to set this value for the cutoff (for the pairlistdist; I
> set 25).
>
> regards from sunny Berlin.
> Ciao
>
> Rita
>
>
> -------- Original-Nachricht --------
> Datum: Thu, 17 May 2007 11:09:56 +0200
> Von: Luca <bellucci14_at_unisi.it>
> An: Rita Cassia <Rita.Cassia_at_gmx.de>
> Betreff: Re: namd-l: Minimization
>
> > On Wednesday 16 May 2007 19:19, you wrote:
> >
> > Hi Rita,
> >
> > 1- I think that you should see your config file and check cutoff distance
> > for
> > nonbondend forces.
> > A very good/standard choice is cutoff 10 and pairlistdist 12 o 14. See
> > manual
> > NAMD 2.6 pag.43
> > You can use margin command for increase margin.
> > 2- You have an initial system that are not in a minimum of potential
> >
> > Luca
> >
> > > Dear NAMD Users,
> > >
> > > I am trying to minimize a complex in a waterbox, following the same
> >
> > steps
> >
> > > for previous simulations with pheophorbides.
> > >
> > > But, the simulation stops with the message :
> > >
> > > "ERROR: Margin is too small for 1 atoms during timestep 741.
> > > ERROR: Incorrect nonbonded forces and energies may be calculated!
> > > FATAL ERROR: Bad global exclusion count!"
> > >
> > > Another thing is: in the configuration file, I set the temperature at 0
> > > Kelvin and , for minimization, I put "reinitvels $temperature"
> > >
> > > which I understand that, after 100 steps, the velocities and
> > > temperature should be reset to 0. But what I get is always values much
> > > bigger than 0 (at the first minimization step, I get 212 K, for
> > > example). Can someone clarify me this point?
> > >
> > >
> > > I am attaching the conf. file and I would appreciate a lot if someone
> >
> > can
> >
> > > help me.
> > >
> > > Thanks in advance.
> > >
> > > Rita Leite

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