Dear Harianto,
Can you send me the output file. Having taken a closer look at the
process_mdout script it seems to me that it creates a summary.volume file
even when the volume is not reported in the output file. Hence you get a
file of a single column (the time) and nothing else. If you then plot this
with xmgr it happily plots you a straight line of Time vs entry in file.
Hence your simulation is probably fine and it is just the extraction program
creating an 'empty' file. Check the mdcrd file and restrt files, the box
size should remain constant.
All the best
Ross
/\
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|\oss Walker
| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
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> -----Original Message-----
> From: owner-amber.scripps.edu
> [mailto:owner-amber.scripps.edu] On Behalf Of Harianto
> Sent: 26 January 2005 15:20
> To: amber.scripps.edu
> Subject: Re: AMBER: Increasing Volume with ntb=1
>
> Dr. Ross,
> Thanks for quick respond.
> I use VMD to visualise it, the protein still has helices but
> partially
> unfolds.
> Here I attach the rmsd upto 6ns.
> The energies are stable.
> Please your suggestion,
> Harianto.
>
>
> Ross Walker wrote:
> > Dear Harianto
> >
> >
> >>dt = 0.001,
> >
> >
> > At 600K you may be getting integration errors at 1fs even
> with shake turned
> > on. I don't know for sure here but it is worth thinking about.
> >
> > If you visualise the simulation what does it look like? Does it look
> > unstable. It is possible you r system is blowing since I
> can see nothing
> > obviously wrong with your input file.
> >
> > What do you get if plot temperature vs time and energy vs
> time? Is the
> > system equilibrating.
> >
> > I suspect the problem with the volume may be due to other
> problems in your
> > simulation.
> >
> > If you can send the complete output file it would be much
> more helpful.
> >
> > All the best
> > Ross
> >
> > /\
> > \/
> >
>
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Received on Wed Jan 26 2005 - 23:53:00 PST
