AMBER Archive (2005)

Subject: Re: AMBER: Increasing Volume with ntb=1

From: Harianto (harianto_at_mailer.sb.fsu.edu)
Date: Wed Jan 26 2005 - 17:19:59 CST

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
>
> /\
> \/
>


  • application/postscript attachment: rmsd.ps



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