AMBER Archive (2009)

Subject: Re: [AMBER] LES and NEB problem

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Wed Oct 14 2009 - 09:14:04 CDT

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
>
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber