SPAM calculations using acetonitrile in cpptraj

[DDGmichigan]

Hi, Hi, I was trying to find out whether we could use SPAM (equations) for calculating interaction energies for small solvent molecules apart from Water, for example if i have a SILCS type solvent mixture 1 M benzene in water and then soak the protein in that solution. I could use SPAM to calculate interaction energies of benzene molecules in the specific environment. The bulk energies can be calculated by pure water +probe boxes simulation. Is it viable?

[drroe]

I don't see any reason why this shouldn't work from a code perspective - nothing in spam is hard-coded for water. You'll probably have to adjust some of the parameters like site_size etc.

[drroe]

Since I haven't heard otherwise, I'm going to assume things have worked and will close this. If not, feel free to reopen and comment.

[DDGmichigan]

Hi Dan,

For estimating the free energies for acetonitrile solvent instead of water, I have to calculate dgbulk and dhbulk for acetonitrile molecules, SO I need to simulate a pure box of C3N molecules to estimate that?

[DDGmichigan]

[drroe]

Will reopen until segfault is resolved.