AMBER Archive (2008)

Subject: Re: AMBER: Using mdcrd files to look at minor charge changes

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On Thu, Apr 03, 2008, Cooper, Matthew wrote:

> I am calculating free energies of solvation using thermodynamic
> integration on amber 7 for a number of small molecules.
> Each time I change the charges on these small molecules I need to rerun
> the simulations to get the numbers for the free energy calculation.
> I would like to use the saved mdcrd files along with a new topology
> files to estimate the free energy value since the partial charges
> differences should not change motion nor the explicit water positions
> all that drastically.

"All the drastically" is pretty relative. I don't see how you can avoid
re-doing the simulations with the correct charges if you want reliable (or
even iterpretable) results.

> I am fine when I just want to get energies but when I use icfe=1 (along
> with a clambda value) to try and get the dv/dl values to output, I get a
> core dump.

We would have to know a lot more about exactly what you did before we could
tell what might be causing a core dump.

...dac

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