[AMBER] neb/amber 10

From: Guillermina Estiu <gestiu.nd.edu>
Date: Wed, 03 Mar 2010 14:12:05 -0500

I am trying to find the path between two conformations of a same
molecule (~5000 atoms) using NEB in AMBER10.
I've prepared the .top and .crd files using addles, following the
instructions given in the manual. It worked after increasing maxdih, for
a maximum number of 14 copies.

Again, according to the manual, I used the input file in the tutorial
(Ross Walkerís) to heat up the system.

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,
&wt type='TEMP0', istep1=0,istep2=35000,
value1=0.0, value2=300.0
&wt type='END'

Running the sander.LES.MPI executable, with my system size, results in
the error:

LES parameters were found

I found the MAXLESADJ parameter to be set to a value of 3000000. I am
not sure if I just have to increase the value. Iíve found some
discussion on the list but not clear answer for this.

I have tried the test case of the tutorial, addles works perfectly but
crash with an error: Floating point exception signaled at 7170b9:
integer divide by zero.

There seems to be two different issues here, one related to the size of
the system. I have seen several posts like this one in the list but not
the solution. Any help on this?


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Received on Wed Mar 03 2010 - 11:30:02 PST
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