AMBER Archive (2007)

Subject: AMBER: Problem with anisotropic pressure scaling

From: Linda Prengaman (lindap_at_cmu.edu)
Date: Fri Mar 16 2007 - 08:23:30 CST

Dear Fellow AMBER Users:

I am trying to do a constant pressure MD run on a DMPC lipid bilayer. I would like to set ntp=2, as that seems more appropriate for membrane simulations. However, when I try to run the simulation, I get the following error message in the output file:

Unit 5 Error on OPEN: lipid_only_constP_NTP.in

This is a pmemd run (amber7).
I also get the following error in the nohup.out file (I am using no hookup)

  Unit 5 Error on OPEN: lipid_only_constP_NTP.in
[0] MPI Abort by user Aborting program !
[0] Aborting program!
p0_11748: p4_error: : 1
Killed by signal 2.
Killed by signal 2.
Killed by signal 2.
Killed by signal 2.
Killed by signal 2.
Killed by signal 2.
Killed by signal 2.
/usr/local/mpich-1.2.4/bin/mpirun: line 1: 11748 Broken pipe

The exact same job with ntp=1 runs with no error message.

Here is the input file in question:

&cntrl
        nstlim=100000,
        imin=0,nscm=1000,
        nmropt=0,
        ntx=1,irest=0,ntrx=1,
        ntxo=1,ntpr=500,ntwr=500,ntwx=500,ntwv=0,ntwe=0,iwrap=1,
        ntf=2,ntc=2,dt=0.002,
            scnb=8.0,scee=1.2,
        cut=12,ntb=2,
        ntp=2,taup=0.2,pres0=1.0,plevel=2,
        ntt=1,temp0=100,tempi=3,ig=3455476,tautp=1.0
&end
Lipid Constraints
100.0
ATOM 1 5888
END
END

The box is orthogonal, so I don't understand what other problem there could be. Please help.

Thank you,
Linda Prengaman
Department of Chemistry
Carnegie Mellon University

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