AMBER Archive (2009)

Subject: Re: [AMBER] LES and NEB problem

From: Rima Chaudhuri (rima.chaudhuri_at_gmail.com)
Date: Thu Oct 15 2009 - 12:53:41 CDT

Yes, the test cases work fine.

On Thu, Oct 15, 2009 at 11:54 AM, Carlos Simmerling <
carlos.simmerling_at_gmail.com> wrote:

> do the test cases work?
>
> On Thu, Oct 15, 2009 at 12:50 PM, Rima Chaudhuri
> <rima.chaudhuri_at_gmail.com>wrote:
>
> > Hi!
> > LES: I tried using the mdin from $AMBERHOME/test/LES and this fails with
> > the
> > same message as well: LES requires numextra=0
> > I've used AMBER ff03.
> >
> > NEB: The run dies even if ineb=0. It reports the same "Could not find
> cntrl
> > namelist" error.
> >
> > thanks,
> >
> > On Wed, Oct 14, 2009 at 9:14 AM, Carlos Simmerling <
> > carlos.simmerling_at_gmail.com> wrote:
> >
> > > see below
> > >
> > >
> > > On Tue, Oct 13, 2009 at 3:35 PM, Rima Chaudhuri <
> > rima.chaudhuri_at_gmail.com
> > > >wrote:
> > >
> > > > Hello!
> > > >
> > > > LES:
> > > > I am trying to run LES on a small part of my system (4 residue long
> > loop)
> > > > using Amber10. I prepared the necessary input files using addles.
> > > > file rprm name=(X_solv.top) read
> > > > file rcvb name=(X_solv_nve6.rst) read
> > > > file wprm name=(les.parmtop) wovr
> > > > file wcrd name=(les.crd) wovr
> > > > action
> > > > omas
> > > > spac numc=5 pick #mon 191 194 done
> > > > *EOD
> > > >
> > > > sander.LES.MPI starts and then dies with the following message in the
> > > .out
> > > > file: Please find the file attached.
> > > > MPI Timing options:
> > > > profile_mpi = 0
> > > > LES requires numextra=0
> > > >
> > > >
> > > is this message relevant? which force field are you using?
> > >
> > >
> > >
> > > > I've attached the input file, md_nve2les.in, as well. Any help in
> > > helping
> > > > me
> > > > understand why this is happening will be much appreciated.
> > > >
> > > > NEB:
> > > > I am doing a NEB exercise as well. Here, I am working with just the
> > loop
> > > > residues (open as structure 1 and closed as structure 2). I created
> > > > 30copies
> > > > of every atom in the loop. Addles created the needed top and crd
> files
> > > > successfully.
> > > >
> > > > Please find the details of the input file below. Here, the run dies
> > > giving
> > > > the message: "Could not find cntrl namelist".
> > > >
> > >
> > > does the same input work if you set ineb=0?
> > >
> > >
> > >
> > > > &cntrl
> > > > imin = 0, irest = 0,
> > > > ntc=1, ntf=1,
> > > > ntpr=50, ntwx=500,
> > > > ntb = 0, cut = 999.0, rgbmax=999.0,
> > > > igb = 1, saltcon=0.2,
> > > > nstlim = 40000, nscm=0,
> > > > dt = 0.0005,
> > > > ntt = 3, gamma_ln=1000.0,
> > > > tempi=0, temp0=300,
> > > > ineb = 1,skmin = 10,skmax = 10,
> > > > nmropt=1,
> > > > /
> > > > &wt type='TEMP0', istep1=0,istep2=35000,
> > > > value1=0.0, value2=300.0,
> > > > /
> > > > &wt type='END'
> > > >
> > > >
> > > > Thanks!
> > > >
> > > > --
> > > > -Rima
> > > >
> > > > _______________________________________________
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> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > > >
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> > >
> >
> >
> >
> > --
> > -Rima
> > _______________________________________________
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> >
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-- 
-Rima
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