On Mon, Oct 8, 2012 at 9:48 PM, "Γιώργος Λαμπρινίδης" <
lamprinidis.pharm.uoa.gr> wrote:
> Dear users,
>
> I was trying to run a simulation according to Tutorial A11 (Pyranose ring
> puckering)
> When I finish the "finer" run using Implicit solvent i get a restart file,
> containing the final velocities. In order to create the explicit solvent
> job i transform prmtop and inpcrd files to pdb and I use tleap to create
> the solvated files and i export them. With this procedure I loose all
> velocities, so when i try to run the "flooding" procedure using the mdin
> file from the tutorial i get an error "no velocities found", because of
> the "irest =1, ntx =5" command.
> How can overcome this error? Propably i am missing something.
> In the tutorial how from the restart file of implicit solvent someone goes
> to "flooding" using explicit water?
>
The input and output files are bundled in a tarball included as a download
at the top of the tutorial. I would suggest looking through this to try
and find your answer (presumably these input files still work, though I
doubt they've been tested recently).
Unfortunately, the NCSU capabilities have rather fallen out of maintenance
and widespread use, at least among the developers, so getting a more
helpful response may take a long wait (if it comes at all). Your best
friends in this case are likely the input files provided on the website and
the manual.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon Oct 08 2012 - 14:30:03 PDT
