Re: pair interaction of water molecules

From: divya nayar (
Date: Sun Nov 28 2010 - 08:54:43 CST

I am able to reproduce the van der Waal's component of pair interaction
energy by manual calculations. I want to ask how should I change my PME
parameters to tell NAMD to calculate the electrostatic energy between only
those two tagged water moleules in a system of 256 water molecules because
the electrostatic energy for 2 molecules that I am getting is not very much
different from that of between one molecule interacting with all other 255
Also, is there a way I can check the values tht I am getting for
electrostatic energy are correct?

Please guide me. Thanks in advance


On Thu, Nov 25, 2010 at 6:31 AM, Erik Nordgren <>wrote:

> Hi Divya,
> Seems like the discrepancy may be due to your only considering the oxygen
> atoms; in fact, the VdW forces computed by NAMD act between all pairs of
> atoms, including hydrogens, so there will be O-O, O-H, and H-H interactions
> to account for.
> -Erik
> On Wed, Nov 24, 2010 at 4:41 AM, divya nayar <>wrote:
>> hi,
>> I am doing a simulation of 256 water molecules in a cubic box. I want to
>> find the pair interaction energy between two water molecules in this system.
>> In order to check the values I want to check the van der Waal's component of
>> pair interaction energy by manually calculating. I want to ask whther NAMD
>> uses just the LJ potential to calculate the vdW component. I mean are there
>> any other parameters which NAMD takes into account. I read user's guide. In
>> the manual, it just says the LJ potential. My manually calculated values are
>> not matching with those from simulations. My conf file looks like as
>> follows:
>> structure ../../tip4p.psf
>> coordinates ../../tip4p-prod260.coor
>> While calculating the pair interaction between water molecules, does NAMD
>> use center of mass of water for coordinates (coordinates of oxygen)? Because
>> I am using the coordinates of oxygens to do manual calculation.
>> can anyone help me with this?
>> Thanks,
>> Divya
> --
> C. Erik Nordgren, Ph.D.
> Chemistry Department
> University of Pennsylvania

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