VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Fri Jan 19 2007 - 07:51:34 CST

Please note that if you use either method that will give you "h-bond"
energies (use charmm or an arbitrary function in VMD) that you're going
to be calculating an energy that wasn't actually included in your
simulation potential (if you were using CHARMM22/27) so its physical
meaning is murky at best. If you reach that point you may (depending on
exactly what you want the energies for) be better off just giving h-bond
geometries, or calculating the nonbond interaction elements that
actually were in your simulation.
Peter

Himanshu Khandelia wrote:
> In addition, you can take your dcds to charmm, which has an explicit
> function to calculate h-bonding energy. You will need the par_hbond.inp
> file. Check the charmm documentation hbonds.inp. But it might be easier to
> do what Peter suggests if you are not familiar with charmm
>
>
>
>> Hi Amit,
>> this depends on what you mean by hbond energy. If you're using a modern
>> CHARMM forcefield, there *is* no hbond energy -- they're implicit in the
>> electrostatic and VDW interactions. You can use namdenergy to get the
>> nonbond interactions between these residues, or write your own script to
>> take the coordinates in vmd and run them through an arbitrary energy
>> function over the trajectory.
>>
>> Peter
>>
>> amit dong wrote:
>>
>>> Hi,
>>> I need to calculate H-bond energy between a pair of residues for the
>>> whole trajectory. I was wondering if there is any quick way of doing it.
>>> Thanks
>>> Amit
>>>