I suggest going through the variables that you specify and make sure they
are what you want.
for example, you specify an initial temperature of 0 and thermostat
temperature of 274, but you also turn off the thermostat (ntt=0) so this
would stay at 0K, which is likely not what you want. You also select a
barostat, but don't use it (ntp=0). ntmin is specified, but minimization is
not used (imin). maxcyc is set (minimization), but not nstlim (md). These
can make it difficult to debug. Use only the flags that you want. Once you
have it cleaned up, see if it runs.
On Sun, Apr 10, 2022 at 4:35 PM erik zuiderweg <zuiderwe.umich.edu> wrote:
> Amber 20 / AmberTools21. on MacOS 11.6
>
> The following script works fine
>
> cat <<eof > mdin
> minimize structure
> &cntrl
> imin=1, maxcyc=10000,ntmin=2,
> cut=300.0, igb=0,
> ntpr=10, ntx=1, ntb=0,
> ntr=1, restraintmask='.1-22810',
> restraint_wt=0.1,
> &end
>
> eof
> sander -O -i mdin \
> -c 2qmt.crd -p 2qmt.parm7 -ref 2qmt.crd -o 2QMT_MIN.out -r 2QMT_MIN.rst
>
>
>
> BUT:
>
> The following script starts but then stops w/o error message
>
> cat<<EOF > mdin
> md for gb1/opc
> &cntrl
> imin=0, maxcyc=500, ntmin=2, nscm=20000,
> ntpr=10000, ntwx=1000, ntwprt=846, ntwr=1000000, cut=9., ioutfm=1,
> ntxo=2,
> ntx=1, irest=0, tempi=0., temp0=274.,
> ntt=0, gamma_ln=0.,
> ntb=1, ntp=0, ntc=2, ntf=2, tol=0.0000001, barostat=2,
> nstlim=5000000, dt=.001, ig=-1, ntave=0,
> ntr=1, restraint_wt=0.1, restraintmask="!:NA,CL,WAT&!.H=",
> /
> &ewald
> dsum_tol=0.000001,
> /
> EOF
>
> sander -O -i mdin \
> -p ../2qmt.parm7 -c ../2QMT_MIN.rst -ref 2QMT_MIN.rst -o
> 2QMT_MIN_MD1.out -r 2QMT_MIN_MD1.rst
>
>
>
>
>
>
> Any ideas?
> Erik Zuiderweg
> Gelrestraat 17b
> 6585XW Mook, Nederland
> 0611154835
>
>
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>
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Received on Mon Apr 11 2022 - 05:30:02 PDT
