Re: NAMD2.7/MEtadynamics simulation analysis disparity

From: felmerino_at_uchile.cl
Date: Thu Apr 29 2010 - 20:49:34 CDT

Maybe this is silly, but remember that in NAMD tha numbering scheme starts with 1 (as in the PDB) while in VMD starts at 0. This sometimes confuses some people when comparing data from the two sources.

best

felipe

----Mensaje original----

De: neville_forlemu_at_yahoo.com

Fecha: 29-04-2010 14:30

Para: <namd-l_at_ks.uiuc.edu>

Asunto: namd-l: NAMD2.7/MEtadynamics simulation analysis disparity

Hello guys,

I have a question about running metadynamics with NAMD 2.7b2. I am running simulations between a ligand and a protein using metadynamics and NAMD2.7. However for some reason there seems to be some problems with the dynamics. For example the distance between the center of mass (COM) of the binding pocket of the protein, and the ligand is not exactly the same between the data obtained during the simulation, and the distances measured by VMD using the save trajectories.

There is a 0 to 1.0 angstroms difference. Secondly the CV seems to suggest that the ligand moves by an average of 6 A in the binding pocket, but this is not apparent from the movie.

So my question is whether someone using NAMD2.7/metadynamics module has experienced this also, and secondly whether there is a reason for this disparity.

Will appreciate any
 insights

Thanks
Neville

      

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