ok- you probably want to use extensive restraints during MD.
On Wed, Jun 15, 2011 at 9:57 AM, <tdo.chem.ucsb.edu> wrote:
> Hi Dr. Simmerling,
>
> Thank you. Yes I am aware of the issues you mentioned in the last
> reply. I am interested in structures in vacuum, so we think high
> temperatures are needed to explore different conformations.
>
> Thank you,
>
>
>
>
>
> Quoting Carlos Simmerling <carlos.simmerling.gmail.com>:
>
> > Dan Roe can probably answer about the error- but are you sure you want to
> > run at 2100K? There are many, many things that can go wrong in
> simulations
> > at such a high T, and it's not clear that it's needed.
> >
> > just want to make sure you know what you're doing, if you are aware of
> the
> > issues then it's fine of course!
> >
> >
> > On Wed, Jun 15, 2011 at 9:49 AM, <tdo.chem.ucsb.edu> wrote:
> >
> >> Hi,
> >>
> >> I am running REMD and use ptraj to extract trajectories from mdcrd
> outputs.
> >>
> >> Here is the script
> >>
> >> trajin ./remd.00 remdtraj remdtrajtemp 300.0
> >> trajout traj300K.dat pdb append
> >>
> >> It works fine until recently I get some messages:
> >>
> >> REMDTRAJ: Final repTemp value read= 1043.840000, set 302
> >> Could not find target 300.000000 in any of the replica trajectories.
> >> Check that all replica trajectory files were found and that
> >> none of the trajectories are corrupted (e.g. missing a temperature).
> >> ptrajProcessInputCoordinates(): Target replica temperature not found
> >> in traj! 100%
> >>
> >>
> >> PTRAJ: Successfully read in 301 sets and processed 301 sets.
> >>
> >>
> >> It only happens to 2/5 of my simulations that I am running (5
> >> different systems using identical method). It seems that ptraj can
> >> only read 300/450 sets of trajectories. So I wonder if this happens
> >> due to something wrong in my simulations, or ptraj itself.
> >>
> >> My simulation has max temp ~ 2100K, in vacuum.
> >>
> >>
> >> Thanks,
> >>
> >>
> >>
> >> --
> >> Thanh D. Do
> >> Department of Chemistry & Biochemistry
> >> University of California Santa Barbara
> >> Santa Barbara, California, 93106
> >>
> >>
> >>
> >>
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>
>
> --
> Thanh D. Do
> Department of Chemistry & Biochemistry
> University of California Santa Barbara
> Santa Barbara, California, 93106
>
>
>
>
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Received on Wed Jun 15 2011 - 07:30:02 PDT
