AW: namd simulation​:protein,l​igand,lipi​d,water and ions

From: Norman Geist (
Date: Thu Aug 30 2012 - 02:06:14 CDT



if you haven’t used the wrapAll or wrapWater commands in this simulation, the output will not show the periodic boundary condition.


Basically the following command should do what you want after loading the the psf and trajectories, but double check and look to the manual :


vmd> pbc wrap –all –compound res –center com –centersel ”protein”


If that doesn’t work, pls send me a pdb of one frame, so I can see what you mean exactly.


Norman Geist.


Von: [] Im Auftrag von Marlet Martinez
Gesendet: Dienstag, 28. August 2012 19:30
Betreff: namd-l: namd-l: namd-l: namd simulation​:protein,l​igand,lipi​d,water and ions



Dear NAMD users,


Recently I ran a simulation that consits of protein, ligand, lipid, water and ions. It was quite complicated to run it, I had to run several different simulations,inactivated "tcl forces"in the second configuration file and I could run my simulation, however now that I am analyzing my trayectory (last restart coord file) I found that something wrong happened because lipid membrane and protein were compacted and waters are all separated from the protein,


Do you have any suggestion?


Thanks in advance,



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