AMBER Archive (2007)

Subject: Re: AMBER: heating up system

From: Adrian Roitberg (roitberg_at_qtp.ufl.edu)
Date: Tue Aug 28 2007 - 13:45:26 CDT

Francesco,

is it really a puzzle that this works:

> Hold the EQE fixed with strong restraint
> 500.0
> RES 1
> END
> END

but this does not: ?

> Keep EQE fixed with weak restraint
> 10.0

you never finished the input !

Francesco Pietra wrote:
> 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
> &cntrl
> imin=1, maxcyc=1000, ncyc=500,
> ntb=1, ntr=1, cut=10.0
> /
> Hold the EQE fixed with strong restraint
> 500.0
> RES 1
> END
> END
>
> Classical minimization
> &cntrl
> 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 heat1.in:
>
> Stage 1 heating of solute/solvent
> &cntrl
> 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,
> cut=10.0,
> nstlim=10000, dt=0.0015,
> ntpr=100, ntwx=100, ntwr=1000
> /
> Keep EQE fixed with weak restraint
> 10.0
>
> This first step with
>
> mpirun -np 4 $AMBERHOME/exe/sander.MPI -O -i heat1.in -o heat1.out -p
> EQE.prmtop -c min_classical.rst -r heat1.rst -x heat1.mdcrd -ref
> min_classical.rst
>
> 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
> EQE.
>
> Thanks
>
> francesco pietra
>
>
>
> ____________________________________________________________________________________
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-- 
                            Dr. Adrian E. Roitberg
                              Associate Professor
               Quantum Theory Project and Department of Chemistry

University of Florida                         PHONE 352 392-6972
P.O. Box 118435                               FAX   352 392-8722
Gainesville, FL 32611-8435                    Email adrian_at_qtp.ufl.edu
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