I would like to thank everyone for the replies. I changed ntx to ntwx and
this solved the issue.
On Wednesday, 6 January 2021, Roitberg,Adrian E <roitberg.ufl.edu> wrote:
> you need ntWx set to a number lower than nstlim. try setting it to 100
> maybe
>
>
> Sent from my iPad
>
> > On Jan 6, 2021, at 09:58, K Jan <10dunajkr.gmail.com> wrote:
> >
> > [External Email]
> >
> > This is the input : (
> > &cntrl
> > ntf=2, ntb=1, cut=12.0,
> > nstlim=5000, dt=0.002,
> > tempi=0.0,temp0=100.0, ntt=1,
> > ntc=2,
> > imin=0, irest=0, ntx=1,
> > ntr=1,
> > restraint_wt=50.0,
> > restraintmask=':1-32'
> > &end )
> >
> > I have ntx =1 so that shouldn`t be a problem
> >
> >> On Wed, 6 Jan 2021 at 14:26, Carlos Simmerling <
> carlos.simmerling.gmail.com>
> >> wrote:
> >>
> >> can you provide your input file md1.in?
> >> it may be that your ntwx is not set to output snapshots to the
> trajectory
> >> file.
> >>
> >>> On Wed, Jan 6, 2021 at 7:58 AM K Jan <10dunajkr.gmail.com> wrote:
> >>>
> >>> Dear all amber users
> >>>
> >>>
> >>> I have been simulating a molecule on Amber and I was wondering whether
> I
> >>> could ask you a question as I am unsure of how to visualize my molecule
> >>> with the output files that I have received from my sander code.
> >>>
> >>> I`ve completed analysis on the molecule by calculating the density,
> >> volume,
> >>> pressure , radius of gyration and the Root Mean Square Deviation.
> >>>
> >>> I would like to use vmd to view the molecule at the different times of
> >> the
> >>> simulation ( simulation lasted 80 picoseconds , and it was completed in
> >>> steps of 10ps) . However, I don`t have any trajectory output files so I
> >> am
> >>> not sure how to do this.
> >>>
> >>> This is my sander code:
> >>>
> >>> sander -O -i md1.in -o md1KCL.out -inf md1KCL.inf -c lr16wKCL.k.minw2
> >> -ref
> >>> lr16wKCL.k.minw2 -r lr16wKCL.k.md1 -p lr16wKCL.k.top -x
> lr16wKCL.k.md1.x
> >> -e
> >>> lr16wKCL.md1.ene &
> >>>
> >>> and the output files I get are:
> >>>
> >>> lr16wKCL.k.md1, md1KCL.inf and md1KCL.out
> >>>
> >>>
> >>> I have also tried running the code by using lr16KCL.k.nc after -x but
> >> this
> >>> doesn’t work either.
> >>>
> >>> I need lr16wKCL.k.md1.x in order to view the molecule in the vmd but
> for
> >>> some reason this code doesn’t output this trajectory file.
> >>>
> >>> Unless, does the lr16wKCL.k.md1 output file contain the trajectory and
> >> can
> >>> I use this in lieu of the explicit trajectory file ?
> >>>
> >>>
> >>> many thanks,
> >>>
> >>>
> >>> Kris J Duna
> >>>
> >>>
> >>> --
> >>> null
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Received on Wed Jan 06 2021 - 07:30:03 PST
