Hi Brian
I can use same coordinates and get a Gromacs topology and no problem with
that but I am just trying to understand how both Gromacs and Amber differs
in initial guess and we can see a big difference in initial box volumes
(keeping solute, water buffer parameters same). Certainly Amber and Gromacs
have different 'philosophy' about this, just want to know that.
Also thanks for sharing VMD alternative option.
regards,
Jiom
On Wed, Jun 18, 2014 at 3:09 PM, Brian Radak <radak004.umn.edu> wrote:
> Is there a reason you cannot (or do not want to) convert the same starting
> coordinates/topologies between the two programs?
>
> I know that many people/groups have developed fairly robust conversion
> scripts for AMBER/GROMACS (off the top of my head I believe I recall
> Michael Shirts distributing a Perl script for this, but that was probably a
> decade ago).
>
> Regards,
> Brian
>
> P.S. Another alternative that I have used for non-orthorhombic/octahedral
> boxes is to build a water box first (for some reason I always used VMD for
> this) and just concatenate the solute/solvent before loading into tleap.
> Your molecule will of course not be "solvated" as such due to overlaps, but
> you can delete waters etc. This is not a quick solution, but it works with
> enough patience.
>
>
> On Wed, Jun 18, 2014 at 9:43 AM, newamber list <newamberlist.gmail.com>
> wrote:
>
> > Hi All
> >
> > Thanks for you replies. Yes I agree choosing same number of water and box
> > shape initially should converge to similar final equilibrated densities
> and
> > volumes with Amber and Gromacs. But I would like to know how AMBER
> differs
> > in adding waters compared to Gromacs as a initial guess (earlier I copied
> > mail from Gromacs archive explaining how initial water box is created by
> > Gromacs)
> >
> > Thanks
> >
> >
> > On Sun, Jun 15, 2014 at 4:52 PM, David A Case <case.biomaps.rutgers.edu>
> > wrote:
> >
> > > On Sun, Jun 15, 2014, newamber list wrote:
> > >
> > > > command: solvateoct hex20 TIP3PBOX 12.0
> > >
> > > Note that this command is only intended to give a *very rough* starting
> > > structure for further simulation. The number of water molecules chosen
> > > for a
> > > given box size (or buffer size) will be very different from what you
> will
> > > get
> > > after equilibration: the number of waters will stay the same (of
> course),
> > > but
> > > the size of the box will change a lot.
> > >
> > > If you choose the same number of waters in Gromacs and Amber, and
> > simulate
> > > to
> > > equilibrium at some temperature, you should get the same average
> > properties
> > > (such as density). In Amber, at least, the equilibrated density will
> be
> > > very
> > > different than the initial density. No one in the Amber community has
> > not
> > > (yet) felt a big need to improve the initial guess that LEaP provides.
> > >
> > > ....dac
> > >
> > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> ================================ Current Address =======================
> Brian Radak : BioMaPS
> Institute for Quantitative Biology
> PhD candidate - York Research Group : Rutgers, The State
> University of New Jersey
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> Integrative Proteomics Room 308
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Received on Wed Jun 18 2014 - 08:00:02 PDT
