Re: AMBER: MD Equil

From: David A. Case <>
Date: Mon, 3 Nov 2003 16:55:59 -0800

On Mon, Nov 03, 2003, Chenglong Li wrote:
> I tried a warm-up of a protein/ligand complex with ibelly=1 and
> NTB=0 using ipol=1 (polarizable ff):
> a) if eedmeth=5, stop at "bad eedmeth in ew_short_dip: 5";
> b) if eedmeth=4, stop at "vlimit exceeded for step 5 ........".
> However, if ipol=0 (turn off). it runs.

Did you minimize first? Minimize with nonpolarizable first, then turn on
polarizability? Use a time step no greater than 0.001 ps?

It's not clear if you have water or not. It probably makes little sense
to go to the trouble of using a polarizable force field if you are not going
to carefully model the solvent environemnt as well. For us, this has almost
always meant doing periodic simulations, not non-periodic ones. So you would
be charting new territory here....


David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
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Received on Wed Nov 05 2003 - 13:53:02 PST
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