From: Gorka Lasso (gorka.lasso_at_gmail.com)
Date: Thu Sep 13 2012 - 03:19:42 CDT

Hi Chris,

Well, actually both. I have never set up an implicit solvent simulation and
I don't know if an MDFF simulation requires any particular parameter
setting using the implicit solvent.

For example, the automatically generated mdff_template specifies the
following force field parameters in explicit solvent:

margin 0
cutoff 10.
switchdist 9.
pairlistdist 11.

but these are different from what Eduardo kindly described.

margin 3
cutoff 16
switchdist 15
pairlistdist 17.5

Most importantly, the mdff_template already set up the gridForceFile
parameter to the gridpdb file that couples the alpha atoms of the protein
to the density map:

  gridForce on
  *gridForceFile $GRIDPDB*
  gridForceCol O
  gridForceChargeCol B
  *gridForcePotFile $GRIDFILE*
  *gridForceScale $GSCALE $GSCALE $GSCALE*

so these does not seem compatible with what Eduardo suggested:

  gridforce yes
  *gridforcefile 10FGFs.pdb*
  gridforcecol O
  gridforcechargecol B
  *gridforcepotfile 10FGF.average.dx*
  gridforcevolts no
 * gridforcescale 0.1 0.1 0.1*
  gridforcecont1 yes
  gridforcecont2 yes
  gridforcecont3 yes

So I am guessing that there must be two different grid-forces to be applied
in MDFF simulations using the implicit solvent?

Best

gorka

On 12 September 2012 19:03, Chris Harrison <charris5_at_gmail.com> wrote:

> Can you be more specific? Do you mean setup an Implicit Solvent
> simulation in general, or are you asking if there are MDFF-specific
> settings that are needed when also using Implicit Solvent?
>
> Chris
>
> On Wed, Sep 12, 2012 at 10:54 AM, Gorka Lasso <gorka.lasso_at_gmail.com>
> wrote:
> > Dear all,
> >
> > I have noticed that the latest version of NAMD permits to run MDFF
> > simulations in implicit solvent. However, the MDFF tutorial does not yet
> > explain how to set up the system in such conditions. I would be most
> > grateful if someone could let me know where to find the corresponding
> > information.
> >
> > Best,
> >
> > Gorka Lasso
> >
> >
>
>
>
> --
> Chris Harrison, Ph.D.
> NIH Center for Macromolecular Modeling and Bioinformatics
> Theoretical and Computational Biophysics Group
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
>
> http://www.ks.uiuc.edu/Research/namd Voice: 773-570-6078
> http://www.ks.uiuc.edu/~char Fax: 217-244-6078
>

-- 
<-------------------------------->
-) Gorka Lasso Cabrera (-
* www.gorkalasso.com *
<--------------------------------->