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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> >
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Received on Wed Jan 06 2021 - 07:00:03 PST
