AMBER Archive (2009)

Subject: [AMBER] LES and NEB problem

From: Rima Chaudhuri (rima.chaudhuri_at_gmail.com)
Date: Tue Oct 13 2009 - 14:35:37 CDT

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

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".
&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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