Re: AW: Periodic Box Dimension (WrapAll is on)

Date: Tue Jan 20 2015 - 01:37:18 CST

Thank you for the comments,
Based on my humble knowledge, when an atom crosses the boundry should enter from the other side. So,during an MD with pbc , all atomic coordinates in the dcd file should lay within the box dimension.

 However, VMD showes some atoms sticked out of the box. I know that VMD does not do magic , simply reads coordinates from NAMD dcd and display them. 
I can not figure out why NAMD produce atomic coordinates which lay out of the box.
I know , i am doing some thing stupid, would you mind to clarify on " wrapping is only a “output”option"?
By the way, i am an chem eng and new to MD technique.

      From: Norman Geist <>
 Sent: Tuesday, 20 January 2015, 10:09:59
 Subject: AW: namd-l: Periodic Box Dimension (WrapAll is on)
#yiv2606044967 #yiv2606044967 -- _filtered #yiv2606044967 {font-family:Helvetica;panose-1:2 11 6 4 2 2 2 2 2 4;} _filtered #yiv2606044967 {panose-1:2 4 5 3 5 4 6 3 2 4;} _filtered #yiv2606044967 {font-family:Calibri;panose-1:2 15 5 2 2 2 4 3 2 4;} _filtered #yiv2606044967 {font-family:Tahoma;panose-1:2 11 6 4 3 5 4 4 2 4;}#yiv2606044967 #yiv2606044967 p.yiv2606044967MsoNormal, #yiv2606044967 li.yiv2606044967MsoNormal, #yiv2606044967 div.yiv2606044967MsoNormal {margin:0cm;margin-bottom:.0001pt;font-size:12.0pt;}#yiv2606044967 a:link, #yiv2606044967 span.yiv2606044967MsoHyperlink {color:blue;text-decoration:underline;}#yiv2606044967 a:visited, #yiv2606044967 span.yiv2606044967MsoHyperlinkFollowed {color:purple;text-decoration:underline;}#yiv2606044967 span.yiv2606044967E-MailFormatvorlage17 {color:#1F497D;}#yiv2606044967 .yiv2606044967MsoChpDefault {font-size:10.0pt;} _filtered #yiv2606044967 {margin:70.85pt 70.85pt 2.0cm 70.85pt;}#yiv2606044967 div.yiv2606044967Section1 {}#yiv2606044967 [] Im Auftrag von JAVADNOROOZI
Gesendet: Dienstag, 20. Januar 2015 06:55
An: NAMD list
Betreff: namd-l: Periodic Box Dimension (WrapAll is on)   Hi,   Hey,   As far as i know NAMD does not wrapatomic coordinates to the other side of the box until the center of mass of themolecule composed of those atoms pass  the boundary.   well as far as I knowNAMD wrapps _EVERY_ atom that crosses the boundary, when wrapping isenabled. As this is often not comfortable, people usually turn of wrapping inNAMD and wrap later in VMD with much more options.   The question is what would happen if one specify the periodic boxdimension much smaller than the max-min of the initial coordinatefile(#.coord)?   In this case center of mass of some molecules stick out the box,does NAMD wrap them to the other side in the very first step?   What if some atoms in a molecule stick out (not the moleculecenter of mass ) of box?   What happens is thatyour simulation will very likely crash because of superimposed atoms and veryhigh VDW energy, as for those atoms sticking out of the box now, there’s nospace on the other side of the box. Please also notice that wrapping is only a “output”option. The simulation itself will always handle the atoms periodic, if a boxis set at all. Seems that you have some critical misunderstanding in some ofthe fundamentals of molecular dynamics simulation.   What are you trying todo?

   Thanks, Javad    


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