RE: AMBER: Increasing Volume with ntb=1

From: Ross Walker <>
Date: Wed, 26 Jan 2005 12:42:13 -0800

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

If you can send the complete output file it would be much more helpful.

All the best

|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- |
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> -----Original Message-----
> From:
> [] On Behalf Of Harianto
> Sent: 26 January 2005 12:12
> To: AMber
> Subject: AMBER: Increasing Volume with ntb=1
> Hi Amberians,
> Please help me to get out of my confusion. I ran high temperature
> simulation, using amber7, ntt=1 T=600K.
> Also I provided constant volume NTB=1, periodic bc.
> When I made a plot for the volume upto few hundreds picosec,
> the graph is a linear with positive gradient.
> (Files are attached : summary.Volume plot.)
> Can somebody explain me why or give me suggestion how to write the
> correct input file ( I expected a constant volume of box in a
> periodic bc.
> Thanks in advance,
> Harianto.

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Received on Wed Jan 26 2005 - 20:53:00 PST
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