Re: AMBER: Increasing Volume with ntb=1

From: Harianto <>
Date: Wed, 26 Jan 2005 18:19:59 -0500

Dr. Ross,
Thanks for quick respond.
I use VMD to visualise it, the protein still has helices but partially
Here I attach the rmsd upto 6ns.
The energies are stable.
Please your suggestion,

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 - 22:53:00 PST
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