Re: dissociation in NAMD

From: Peter Freddolino (
Date: Mon Nov 06 2006 - 15:24:02 CST

Hi Sukesh,
this really isn't an appropriate problem for molecular dynamics; if you
want to be doing bond formation/dissociation you really ought to be
using some level of quantum mechanics.

sukesh shenoy wrote:
> Howdy,
> I am having a peculiar problem in NAMD with the dissociation
> of nitromethane. I need to show that the nitromethane(CH3NO2)
> dissociates by the breaking of CN bond and forms methyl nitrite by the
> formation of CO bond. SInce NAMD cannot show dissociation of bonds i
> am using lennard jones parameters to simulate the dissociation.
> However when i provide LJ parameters for both CN and CO, the
> nitromethane molecule deforms with the formation of a bond between CN
> and CO simulaneously. I need NAMD to calculate the distance between CN
> and CO and apply the LJ parameters only to the pair which is closer to
> it. I believe that i will need to go and change the NAMD program
> itself. Can anyone tell me a method to get this done faster?
> Also if anybody has a different approach i would be glad to
> know it.
> Thank you,
> Sukesh
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