[gmx-users] General MD question

Itamar Kass (Med) itamar.kass at monash.edu
Tue Feb 1 10:43:04 CET 2011

Hi Stephan,

It all a matter of time scale. Large molecules ==> slower movements (compare
trucks and motor-bikes).


On 1 February 2011 03:18, lloyd riggs <lloyd.riggs at gmx.ch> wrote:

> Dear All,
> A quick question as I have not really delved into code for gromacs ever,
> nor know anyone close whom has worked on it.
> If I set up an MD simulation using a 4 protein complex, and 1 small
> peptide, plus waters, etc...and run the whole thing the proteins never move,
> only the amino acids within(constant temp RT and pressure 1 bar).
> Two domains make one complex, and another two the other.  Basically, if I
> seperate the domains say 5, 10, 15 angstrom, etc...the amino acids will
> drift (the chains) towards each other, but the two large (global) protein
> units never move their center (I know I can make it work with Pull vectors,
> but why not in the simple system with a generated initial randomized
> velocities), I woundered why they are fixed in a normal run with minimal
> parameters?  Is there a reason (specific to developers), historical reason,
> or other?  As waters move around fine, and anything else added (salt, small
> molecules of 20-30 atoms, water) except the central molecule(s) of interest.
> Grüsse
> Stephan Watkins
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"In theory, there is no difference between theory and practice. But, in
practice, there is." - Jan L.A. van de Snepscheut

| Itamar Kass, Ph.D.
| Postdoctoral Research Fellow
| Department of Biochemistry and Molecular Biology
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