Dear Linda,
This error message is just telling you that you don't that the input
file: lipid_only_constP_NTP.in in the directory where you are trying to
run the job from. Have you renamed it between running with ntp=1, or
have you changed directories and forgotten to copy the revised file
across?
Hope this helps
Andy
On Fri, 2007-03-16 at 10:23 -0400, Linda Prengaman wrote:
> 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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--
Cat, n.: Lapwarmer with built-in buzzer.
+----------------------------------------------------------------------+
| Andy Purkiss-Trew, School of Crystallography,Birkbeck College,London |
| E-mail a.purkiss.mail.cryst.bbk.ac.uk |
+----------------------------------------------------------------------+
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Received on Sun Mar 18 2007 - 06:07:32 PDT
