Re: can you give me more advice about: vlimit exceeded when sander calculate free energies using TI

From: David A. Case <>
Date: Mon, 16 Jun 2003 08:12:05 -0700

On Mon, Jun 16, 2003, sxzheng wrote:

> I have test the system: first, just take the ligand in waterbox it can run
> normally even with TI method second, do the complex's dynamics in capwater
> condition with ibelly=0, it can run normally also with TI method third, do
> the complex's dynamics in capwater condition with ibelly=1, it can run
> normally with no Ti method, but vlimit exceeded with TI method from the
> first step in clambda=0.0.

It looks like the routines in set.f are making modifications for the regular
Hamiltonian, but not for the perturbed Hamiltonian, and this is leading to
memory corruption.

The simple advice is: don't use ibelly in this way; (use ntr=1 instead). You
could try to debug it by not calling the "set" routines and seeing if that

I am still leaning toward removing the ibelly option altogether in future
releases, at least until it can be implemented without so many side effects.

...thanks for your report....dac

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 Mon Jun 16 2003 - 16:53:01 PDT
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