[gmx-users] Topology- make bonds with certain cut-off distance

Erik Marklund erikm at xray.bmc.uu.se
Sat Aug 25 12:13:14 CEST 2012


In case you want the "bonds" to be dynamic I think the only way is to use tabulated interactions. A bit tedious to set up, but doable. Note that this will NOT emulate angles or dihedrals, just the stretching term. I can't understand why you would want bonds between all atoms within a certain distance, however, and I hope you know what you're doing.

25 aug 2012 kl. 06.54 skrev mohan maruthi sena:

> Hi all,
>           I want build a toplogy for a protein , for which , each and
> every atom  has to  make bonds with other atoms with in certain
> specified cut-off distance. How can i do this ?
> Please suggest me a way,
> Thanks in advance,
> Mohan
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Erik Marklund, PhD
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 6688        fax: +46 18 511 755
erikm at xray.bmc.uu.se

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