Re: [AMBER-Developers] iwrap in sander

From: Thomas Cheatham III <>
Date: Mon, 2 Aug 2010 11:04:03 -0600 (Mountain Daylight Time)

> > 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.

Maybe I am dense, but why is this a problem? If the molecule to be
restrained is fixed in space it will never move and never go out of the
box. The only time I can imagine a difficulty is if your molecule to be
restrained spanned the box initially. A simple check could be added to
test for this, but I think it would have to be a very unusual case since
people normally build within the primary unit cell and even if it was
infinite (which isn't supported anyways in terms of B/A/D) the positional
restraints would still work.

The only exception case could be for a very large solute, solvated with
too low a density such that the box shrank in constant P and put the
molecule spaning the box, but then of course it would crash into itself

Am I misunderstanding something here?


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Received on Mon Aug 02 2010 - 10:30:03 PDT
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