[gmx-users] Re: Question about embedding a force field with no torsion term
leafyoung at yahoo.com
Thu Nov 22 06:29:18 CET 2007
Please take some time to get to know what's 1-4 interaction, and what is
In simple words, they are of two types: 1-4 belonging to non-bonded
interaction; torsion is bonded interaction. So in nature, they are not
conflicting each other; The reason why we isolate the definition of 1-4
interaction out of nonbonded interaction is that, non-bonded interaction
exist for every pair of atoms, but for atoms inside one molecule, we
will zero (or "exclude") the interaction between adjacent atoms and 1-3
neighour, and also scaled down 1-4 neighbour interaction to avoid
crashing because they are usually in close distance due to linkage.
So leave the 1-4 interaction and if your forcefield doesn't have
torsion, don't put that in. That's how simple the issue it is if you can
sort things right.
On 11/22/2007 8:55 AM, Mark Abraham wrote:
> Bo Zhou wrote:
>> Thanks, Mark. Can you tell me any more in detail?
> No, because I don't know. However I know where to find out, and I
> pointed you there.
>> I am really somewhat
>> confused about it. I want to cooperate this force field with oplsaa, but it
>> looks strange that there is not any torsion energy at all but can have 1-4
>> interactions. with " nrexcel=2", Do I still need 1-4 interactions made by
>> the procedure of genning pairs? Thanks very much.
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