Re: issue with solute that splits

From: Felipe Merino (
Date: Fri Jun 01 2012 - 14:20:22 CDT



In principle this is not a NAMD concern. As far as i know that is impossible to do "on the fly". In the end the wrap command is just to mantain the original for of the cell on the output. If you wat you molecules rejoint you have to post-process the dcd in VMD. the command is something like pbc wrap -all -centersel yourComplex. The you can further repair any weird thing due to crossing the cell with pbc join (I don't remember exactly the command here). Check the pbcTools manual for VMD.



----Mensaje original----De: 01-jun-2012 14:52Para: "Namd Mailing List"<>Asunto: namd-l: issue with solute that splitsDear all,I would like my solute (made up of a dimeric protein plus a ligand)to be translated as a whole to the other side of the cell, when itcrosses the periodicboundary.As far as I understood, activating the keyword "wrapAll on" in theNAMD config file,all the molecules (which are composed by contiguous atoms) in my systemwill do that, but I would like my complex (monomer + monomer + ligand)to do that as a whole.Let's say when the center of mass of my complex crosses the boundariesof the box,it will be translated on the other side of the cell.Any hint on how I can accomplish this would be really appreciated.Many thanks in advance.Best,-- Dr Massimiliano PorriniInstitute for Condensed Matter and Complex SystemsSchool of Physics &amp; AstronomyThe University of EdinburghJames Clerk Maxwell BuildingThe King's BuildingsMayfield RoadEdinburgh EH9 3JZTel +44-(0)131-650-5229E-mails :

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