Thanks a lot David.
-----Original Message-----
From: "David A Case" <case.biomaps.rutgers.edu>
Sent: 29-07-2014 05:41 PM
To: "AMBER Mailing List" <amber.ambermd.org>
Subject: Re: [AMBER] NONBONDED_PARM_INDEX
On Tue, Jul 29, 2014, Him Shweta wrote:
>
> I dont understand how indexing is done for Nonbonded terms which uses the
> following relation:
>
> index = ICO(NTYPES*(IAC(i)-1)+IAC(j))
>
> For understanding purpose i made a topology file for single water molecule,
> but i could not understand the nonbonded index term that from where the
> values 1, -1, -1, 3 came and what is its meaning.
>
> %FLAG NONBONDED_PARM_INDEX
>
> %FORMAT(10I8)
>
> 1 -1 -1 3
>
It's pretty simple to work out the values for your simple example:
IAC(i) IAC(j) NTYPES*(IAC(i)-1)+IAC(j) ICO(NTYPES*(IAC(i)-1)+IAC(j))
1 1 2*0 + 1 = 1 1
1 2 2*0 + 2 = 2 -1
2 1 2*1 + 1 = 3 -1
2 2 2*1 + 2 = 4 3
IAC(1) is atom type OW; 2 is atom type HW. An interaction between OW and OW
looks in the first position of the CN1 and CN2 arrays to get the Lennard-Jones
parameters. HW--HW looks in position 3. HW--OW and OW-HW would look in
position -1, which is a flag to skip that interaction.
Try some other examples. Water is a bit special, since HW-OW is defined to be
a special type of interaction in the parm.dat file, leading to the -1 index.
(All such interactions are ignored in modern Amber force fields.)
...good luck...dac
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Received on Wed Jul 30 2014 - 05:30:03 PDT
