From: luca (bellucci14_at_unisi.it)
Date: Sat Dec 01 2007 - 03:45:35 CST
I agree with your solution, but I do not know how to make constraint between H or (O) and 4th "phantom" site charge.
At this moment NAMD uses only SHAKE_H algorithm. Am I ok?
When rigidBonds control is set to "all" the bond between each hydrogen
and the heavy atom to which it is bonded is constrained.
When "water" is selected, the Hydrogen-oxygen and
hydrogen-hydrogen distances are constrained ....
.but this is a particular case.
I am sorry but I do not know if there is an alternative solution in NAMD.
> Thanks for response, but I respectfully disagree.
> The solution is oxygen has zero charge and a 4th point is added for the "electron"
> which has no mass. (This is how amber ff and charm ff represent tip4p)
> If one applies shake type bond constraints between hydrogens, oxygens, and the extra point then all should work w/out any extra code. Settle may not work but rigid bonds should.
> The question is how does namd identify hydrogens (code suggests it is based only on mass) and namd allows for H-H bonds (as i the TIP3 rigid contraints)
> -----Original Message-----
> From: luca [mailto:bellucci14_at_unisi.it]
> Sent: Fri 11/30/2007 5:19 PM
> To: Bishop, Thomas C
> Subject: Re: namd-l: tip4p - namd follwup
> Hi Tom,
> You can NOT use TIP4P water model in NAMD.
> Oxygen point charge in TIP4P model
> does not coincide with atom position.
> This type of model require a special computational routine, but this is not in NAMD.
> > Anyone with experience using TIP4p in namd?
> > seems this questions never got answered on the listserv
> > Thanks
> > Tom
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