[gmx-users] removing degrees of freedome from different proteins at different timesteps of an md simulation

Jochen Hub jhub at gwdg.de
Fri Sep 12 07:32:05 CEST 2008

Filip Jagodzinski wrote:
> hi gmx-users,
> i haven't been able to accomplish the following:
> i have a system with n atoms, and i want to remove the degrees of
> freedom for some of the atoms during different moments of the simulation
> for example, assume the primary sequence of my protein is a-b-c-d-e-f-g,
> and, for the first 50 picoseconds, i know that b, c and d move as a
> "group", and so i want to remove the degrees of freedome between b and c
> and between c and d, and have {bcd} move as one unit; then, at time
> 50-100 picoseconds, atoms b, c and d no longer more as a group, but
> atoms d, e, f and g move as a group, so for the integration step from 50
> to 100 picoseoncds, i would want to remove the degrees of freedome
> between d and e, between e and f, and between f and g

I don't think this is possible within a single simulation. You would
have to change your topology for each section of your simulations. You
can add constraints to your topology or, if you want to keep the rigid
parts of the protein a bit flexible, bonds of type 6.

Depending on what you want to do, maybe it could also be sufficient to
fit your simulation on some structure and always use the rigid part as
fit group.

cheers, jochen

> this is similar to fixing all but the active site of a protein and only
> performing md on only the active site, but not quite the same
> any suggestions?
> thanks much!
> filip
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Dr. Jochen Hub
Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
D-37077 Goettingen, Germany
Email: jhub[at]gwdg.de
Tel.: +49 (0)551 201-2312

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