AMBER Archive (2008)

Subject: AMBER: Problem running NEB in AMBER10

From: Chris C. (chris.bc57_at_gmail.com)
Date: Wed Nov 26 2008 - 12:38:17 CST

Hi,
I am trying to find the path between two conformations of a same
molecule (~250 atoms) using NEB (I'm using AMBER10 and have applied
all the latest bugfixes).
I've prepared the .top and .crd files using addles, following the
instructions given in the manual. This step seems OK, as the files are
created.
Again, according to the manual, one shall run sander.MPI for NEB calculations.
I'm using the input file provided by Ross Walker in his NEB tutorial, ie:
NEB Initial MD
 &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'
 /

Sander crashes immediately and here is what I get
| Flags: MPI
  *** THIS VERSION WILL NOT ACCEPT TOPOLOGY FILES
      THAT WERE CREATED BY ADDLES, WITH NPARM=1
      USE A VERSION COMPILED WITH -DLES

I then tried to run my calculation with the sander.LES.MPI executable,
and then another kind of error occurred
LES parameters were found
EXCEEDED MAXLESADJ!

I found the MAXLESADJ parameter to be set to a value of 3000000.
Is my system too big ? If so, should I increase this value and recompile ?

Chris
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