I would also try running this on a single CPU, and carefully checking the
initial rmsd to the refcrd. It's not difficult to make mistakes in setting
masks, etc.
On Dec 31, 2014 9:35 AM, "David A Case" <case.biomaps.rutgers.edu> wrote:
> On Wed, Dec 31, 2014, Pallavi Mohanty wrote:
>
> > I am running TMD in AMBER, at this point i am done with heating and
> > equilibration steps. I have an open and closed conformation and i want to
> > span the transition from open to closed.
> > My Input file for TMD was
> >
> > TMD: open->closed; target rmsd 1.6; resid 38-134 restrained
> > &cntrl
> > imin = 0, ntx = 1, nstlim = 5000, irest = 0,
>
> You are using irest=0, which would not be advised if you have already done
> heating and equilibration. But this is unlikely to be the cause of your
> problem.
>
> > and I got an error stating "Targeted molecular dynamics:
> > tgtrmsd = 1.60000, tgtmdfrc= 1.00000
> > | INFO: Old style inpcrd file read "
>
> This is not an error message. Set ntpr=1 and see if you get any useful
> information from early steps. Make sure that all energies (except the
> targetted stuff, which I assume you are now turning on for the first time)
> are the same in the first step of the new run compared to the final step
> of the equilibration.
>
> ...hope this helps....dac
>
>
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Received on Wed Dec 31 2014 - 07:00:04 PST
