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.mccammon.ucsd.edu>
Date: Monday, May 21, 2007 3:15 pm
Subject: Re: AMBER: Pi-pi interactions
To: amber.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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Received on Wed Jun 06 2007 - 06:07:18 PDT
