AMBER Archive (2007)

Subject: Re: AMBER: LES problem

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Tue Jun 05 2007 - 07:14:15 CDT

it looks ok to me, perhaps you can send prmtop and inpcrd privately (not to
the whole list)
and I can try them.

On 6/4/07, Urszula Uciechowska <urszula.uciechowska_at_pharmazie.uni-halle.de>
wrote:
>
>
> Dear Amber users,
>
> I would like to run LES simulations on an loop. I have the non-les system
> equilibrated (water
> +ions) and I created the LES topology (starting from the equilibrated
> non-LES system) file by
> making 5 copies of my region. After running sander.LES I am getting only
> the empty out file
> and nothing more I checked my prmtop file and it seems to be ok and also
> copies that I made.
> I copied my input file below that I would like to use to LES, maybe there
> are some mistakes.
>
> &cntrl
> imin = 0, irest = 1, ntx = 7,
> ntb = 2, pres0 = 1.0, ntp = 1,
> taup = 2.0,
> cut = 9, ntr = 0,
> ntc = 2, ntf = 2,
> tempi = 298.15, temp0 = 298.15,
> ntt = 3, gamma_ln = 1.0,
> nstlim = 250000, dt = 0.002,
> ntpr = 200, ntwx = 200, ntwr = 2000
> /
>
> sander.LES -i LES_p.in -o LES_p.out -p LES_p.prmtop -c LES.x -r
> LES_p.restrt -x LES_p.mdcrd
>
> Thank you for any help,
>
> Urszula
>
> MSc.PhD Student
> Medicinal Chemistry Group
> University of Halle-Wittenberg
>
> ----- Original Message -----
> From: David Cerutti <dcerutti_at_mccammon.ucsd.edu>
> Date: Monday, May 21, 2007 3:15 pm
> Subject: Re: AMBER: Pi-pi interactions
> To: amber_at_scripps.edu
>
> > No, there are no pi-pi interactions in any of the AMBER
> > forcefields. This
> > is a quantum effect, and is not treated in any classical
> > forcefield.
> > Emulation of this effect can come about only via favorable van-der
> > Waals
> > interactions, and hopefully the physics is not upset by the qq/r
> > point charge interactions.
> >
> > Dave
> >
> >
> > On Mon, 21 May 2007, Roberto Veiga wrote:
> >
> > > Dear all:
> > >
> > > are the Amber force fields suitable to this kind of interaction
> > (pi-pi)?
> > >
> > > []s,
> > >
> > > Roberto
> > > ------------------------------------------------------------------
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-- 
===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor                 Phone: (631) 632-1336
Center for Structural Biology       Fax:   (631) 632-1555
CMM Bldg, Room G80
Stony Brook University              E-mail: carlos.simmerling_at_gmail.com
Stony Brook, NY 11794-5115          Web: http://comp.chem.sunysb.edu
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