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Hi,
I have confusion in defining weight in force field file, what exactly weight is? I did read the http://docs.openmm.org/7.0.0/api-python ... eSite.html but fail to understand fully. How do we calculate these weight factors for some simple molecule like water tip5p? I am asking this because I will use this procedure for my system.
example given below:
<Atom name="O" type="tip5p-O"/>
<Atom name="H1" type="tip5p-H"/>
<Atom name="H2" type="tip5p-H"/>
<Atom name="M1" type="tip5p-M"/>
<Atom name="M2" type="tip5p-M"/>
<VirtualSite type="outOfPlane" siteName="M1" atomName1="O" atomName2="H1" atomName3="H2" weight12="-0.34490826" weight13="-0.34490826" weightCross="-6.4437903"/>
<VirtualSite type="outOfPlane" siteName="M2" atomName1="O" atomName2="H1" atomName3="H2" weight12="-0.34490826" weight13="-0.34490826" weightCross="6.4437903"/>

The equations are given in a slightly more readable form at http://docs.openmm.org/latest/userguide ... tual-sites. But there's no single answer for how you choose them. The virtual site class defines how the site position is chosen based on the particle positions and the weights you provide. It doesn't specify how you should choose those weights.

In the case of an outOfPlane virtual site, weight12 and weight13 set the position within the plane of the three atoms. They give the fraction of the distance along the 1-2 and 1-3 bonds. And then weightCross determines the distance from the plane of the three atoms, as described by the formula.

Hi Peter,

Is it compulsory to define weight factor in force field field? I have water with 5 virtual sites with known position and angles of all sites(total 8 sites)?
As I mentioned in my previous post I have the functional form of the 3body potential energy which depends on the 5 parameters , and these parameters are different for different atoms interactions. I want to implement it using custom-non-bonded force option. Do you have any example for this? It this possible to implement?

I am attaching my potential energy form.

The weights are part of the definition of the virtual site positions. They have nothing to do with the functional form of your interaction. If you have five virtual sites whose positions are computed based on the positions of three atoms, you must know how they're computed? You need to tell OpenMM that. <VirtualSite> tags are how you tell it that. It offers several different rules for computing virtual site positions, as described in the manual. You need to determine whether any of those rules can reproduce the computation you want it to do.

Once the virtual site positions are computed, you then need to compute the energy as a function of those positions. That's what the other tags in the file are for, for example <NonbondedForce> or <CustomNonbondedForce>.