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I have a couple of questions regarding the vdw parameter listings in charmm19:

As I understand, in Charmm22, vdw 1-4 interactions are required for all atom types. If two sets of Emin and Rmin are listed for a given atom type, then the second set of LJ parameters would be used for the 1-4 vdw interactions. Otherwise, the first set would be used.

I would like to know if this same rule also applies to Charmm19?

Thanks in advance for those who reply.

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Look for the keyword NBXMod in nbonds.doc

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Thank you for your reply. I am aware of NBXMod. Is just that the description of it is bit vague, but I subsequently found the previous post that explains it:

http://www.charmm.org/ubbthreads/ubbthreads.php?ubb=showflat&Number=23646

Another reason I ask this is because in the paper reference for CHARMM19 (E. Neria et.al. JCP, vol.5, p1902 (1996)), nonbonded energy terms are considered for all atom pairs except those bonded or separated by a single bond (page 1918). This sounds to me non-bonded atoms separated by two bonds (1-3 interactions) are included for calculations.

I wonder if I have misunderstood something here?

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1-3 interactions are not included. The sentence in the Neria paper is misleading:_ "the sums are over all pairs except those bonded or separated by a single bond" indicates that there are two cases which are excluded; "a single bond" should perhaps have been "two bonds".


Lennart Nilsson
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Good job in finding back that old thread. I already forgot I wrote a clarification on NBXMod blush


Moderated by  alex, lennart, rmv 

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