[gmx-users] Dihedral angle autocorrelation function
samrucu at yahoo.co.in
Wed Jan 28 00:28:45 CET 2015
On Tuesday, 27 January 2015 12:30 PM, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
On 2015-01-27 00:56, atanu das wrote:
> Hi All,
> I am trying to calculate the dihedral angle autocorrelation function by using the following command ----
> g_chi -s md.tpr -f md.xtc -corr -phi -psi
> I get multiple files with autocorrelation functions for individual phi and psi dihedral angles which are really easy to identify as they get saved as corrphiARG2.xvg for phi angle of ARG-2 and so on.
> Now looking at the individual autocorrelation functions I see that most of them don't get to zero and reach a plateau ~0.7 or 0.8 or 0.5. My system is a 11-residue peptide and I simulated the peptide for 1 micro-second in explicit water at 300K. I could have believed the data if the system was simulated for very short time (~1-2 ns). But, I can't convince myself that the autocorrelation function does not reach zero even after simulating for microsecond timescale (this means that the dihedral angle relaxation time is infinity!).
> Could anybody tell me what am I doing wrong?
This is as it should be. It is described in this classic paper ;) D. van
der Spoel and H.J.C. Berendsen: Molecular dynamics simulations of
Leu-Enkephalin in water and DMSO Biophys. J. 72 pp. 2032-2041 (1997)
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
spoel at xray.bmc.uu.se http://folding.bmc.uu.se
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