Re: [AMBER] regarding IWRAP in Sander

From: case <>
Date: Sat, 31 Jul 2010 09:03:17 -0400

On Sat, Jul 31, 2010, aneesh cna wrote:
> 1. Does this IWRAP has anything do with the energetics of the system?. I am
> running a system with position restraint ( 1 kcal/mol ) of few molecules.

Iwrap won't work with position restraints, since the targets of the restraints
are not wrapped, and the ntr=1 code does not use the minimum image idea, if
I remember correctly. cc-ing to the developers' list: we need to either
prohibit this combination (in mdread.f) or make it work correctly.

> 2. In another case, a system with protein in organic solvent, protein is
> flying out of the box when IWRAP = 1. But the system seems to be running
> fine with IWRAP =0.

I don't recognize this, and the description is not precise enough to figure
out what is happening.

Can some developer please check out using unformatted restart files? That
would eliminate most of the need for using iwrap in the first place. Absent
that, someone shold look at desmond's "glue solute molecules" option, which
looks like a smarter version of iwrap.

[Note: the basic problem with iwrap in sander is that makes very simple
assumptions about how the wrapping should be done, which are not always
correct. ptraj offers a lot more flexibility. I've always felt that the
iwrap option in sander/pmemd should be deep-sixed, but I keep getting


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Received on Sat Jul 31 2010 - 06:30:03 PDT
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