[gmx-users] rigid body

Tatiana Hushcha hushcha at bpci.kiev.ua
Thu May 8 16:29:01 CEST 2003

Dear GROMACS developers,

We would like to simulate realistic behavior of the whole human serum
albumin (HSA) molecule at the physiological conditions. We plan to use the
modeled time characteristics of conformational transitions to interpret our
experimental relaxation data, so the simulated times should be correct.

It is our belief that the only way to solve our problem by computational
resources available, is to treat several fragments of HSA molecule as rigid
bodies. We studied Molecular Modeling software available, and GROMACS in
general seems extremely attractive in view of our purposes. But we had no
success in finding in the GROMACS User Manual the feature of treatment the
HSA molecule as a number of rigid bodies. GROMACS Freeze Group concept would
be of use in the case of a single rigid fragment, but employing of several
rigid body fragments is absolutely necessary for us.
So, we would be grateful if you give us explicit confirmation that GROMACS
can't be used to treat a large biomolecule as a system of several rigid
bodies. Or maybe this feature is still available? It may be not documented
yet, for example.

Looking forward to hearing from you.

Best regards,

Dr. Tatiana Hushcha
Institute of Bioorganic Chemistry,
Kiev, Ukraine

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