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
>
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jun 15 2011 - 07:00:04 PDT
