AMBER: heating up system

From: Francesco Pietra <>
Date: Tue, 28 Aug 2007 09:16:57 -0700 (PDT)

Taking the way indicated by Gustavo, Bud and others, to carry out successfully
classical procedures before QM-MD, for a 98-atoms solute EQE in methanol box
(solvatebox EQE MEOHBOX 15), I carried out successfully (Amber9) minimization
of solvent alone, then of the whole system, according to:

Initial minimization solvent
imin=1, maxcyc=1000, ncyc=500,
ntb=1, ntr=1, cut=10.0
Hold the EQE fixed with strong restraint

Classical minimization
imin=1, maxcyc=10000, ncyc=4000,
cut=10.0, ntb=1, ntc=1, ntf=1

Planning to heat-up the system slowly at const volume, with

Stage 1 heating of solute/solvent
imin=0, irest=0, ntx=1,
ntb=1, ntr=1, ntc=2, ntf=2,
tempi=0.0, temp0=50.0,
ntt=3, gamma_ln=1.0,
nstlim=10000, dt=0.0015,
ntpr=100, ntwx=100, ntwr=1000
Keep EQE fixed with weak restraint

This first step with

mpirun -np 4 $AMBERHOME/exe/sander.MPI -O -i -o heat1.out -p
EQE.prmtop -c min_classical.rst -r heat1.rst -x heat1.mdcrd -ref

exited with MPI abort in communicator MPI_COMM_WORLD error code 1.

The attached heat1.out shows that the procedure halted at loading constrained
atoms, though I don't see how to remedy, except by removing the restraint on


francesco pietra

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Received on Wed Aug 29 2007 - 06:07:39 PDT
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