From: sukesh shenoy (sukesh_shenoy_at_yahoo.co.in)
Date: Mon Nov 06 2006 - 11:00:40 CST
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.
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