If you aren't wrapping (iwrap=0) or not using netCDF restart files (ntxo=2,
AMBER12 and later only?), then it is quite common to get overflow
(registered as *s) in restart coordinates after a long period of time. I'm
not sure if that matches the "Permission denied" part of the error message,
but it's advisable anyway.
A similar problem may happen with your mdcrd files unless you use netCDF
outputs there as well (ioutfm=1).
Regards,
Brian
On Mon, Aug 19, 2013 at 12:11 PM, Карлов Дмитрий <dkar89.gmail.com> wrote:
> Dear Amber users,
>
> I am trying to perform a molecular dynamic simulation of sugar/water system
> (about 14000 atoms). Topology creating, minimization and heating were ok,
> but after 60 ns something went bad.
> Jobs are often aborted after ~ 1ns due to error like this: "forrtl:
> Permission denied
> forrtl: severe (38): error during write, unit 16, file ... "
>
> input file:
> constant pressure constant temperature production run
> &cntrl
> nstlim=50000000, dt=0.002, ntx=5, irest=1, ntpr=500, ntwr=10000,
> ntwx=10000,
> temp0=325.0, ntt=3, gamma_ln=1.0, tautp=2.0,
> ntb=2, ntp=1,
> ntc=2, ntf=2,
> ig = -1,
> &end
>
> Then I got .rst file with "*************". Maybe input has internal
> contradictions?
>
> DK
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>
--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Center for Integrative
Proteomics Room 308
Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
radakb.biomaps.rutgers.edu
====================================================================
Sorry for the multiple e-mail addresses, just use the institute appropriate
address.
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Received on Mon Aug 19 2013 - 10:00:02 PDT
