On Fri, Apr 13, 2012, Albert wrote:
>
> I am trying to use the following two .in file for my NVT steps but
> both of them failed with similar errors:
>
> command:
> mpiexec -np 6 $AMBERHOME/exe/sander.MPI -O -i heat.in -p bm.prmtop -c
> mini2.rst -o heat.out -r heat.rst -x heat.mdcrd -ref mini2.rst
>
>
> ------------1.in--------------
> heating gradually over 300ps
> &cntrl
> imin=0,irest=0,ntx=1,
> nstlim=300000,dt=0.001,
> ntc=2,ntf=2,
> cut=10.0, ntb=1,
> ntpr=500, ntwx=500,
> ntt=3, gamma_ln=2.0,
> tempi=0.0, temp0=300.0,
> nmropt=1
> /
>
> Hold the 1-288 fixed
> 50.0
> RES 1 288
>
> &wt TYPE='TEMP0', istep1=0, istep2=300000,
> value1=0.1, value2=300.0, /
> &wt TYPE='END' /
>
> END
Note that the group cards are in the wrong place (they should come last),
and the "END" card needs to come directly after the "RES 1 288" card. All of
these will be ignored here, however, since you are not setting ntr.
>
>
> ----------fail-1.log---------
>
> Assertion failed in file helper_fns.c at line 335: 0
> memcpy argument memory ranges overlap, dst_=0x2b59f9dea970
> src_=0x2b59f9dea970 len_=157944
I don't recognize the helper_fns.c file. Try a short run (say nstlim=3) in
serial, not parallel.
.....dac
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Received on Fri Apr 13 2012 - 20:30:04 PDT
