[AMBER] How best to build a solvent box for a solute with changing dimensions?

From: Kasprzak, Wojciech (NIH/NCI) [C] <"Kasprzak,>
Date: Mon, 7 Aug 2017 15:53:57 +0000

Dear Amber Users,

I am trying to run an explicit solvent simulation with a very flexible RNA solute (akin to a 3-way junction),
parts of which move a great deal outside the primary solvent box (i.e. the solute extents grow considerably).
After a short stage with iwrap=1, a large segment is sticking out of the solvent box, and, more importantly,
the range of large scale motions (angle between the two major branches) observed till the iwrap diminishes.
I am "anchoring" parts of the solute via harmonic restrains to avoid major rotations and translations of the
entire molecule inside the solvent box.

1) How best to build a solvent box big enough to accommodate the expected range of motions of the solute?
    Could I overlay the extreme states observed in implicit solvent runs, create a solvent box around them,
    then remove all but the initial state and "refill the voids" with solvent? What LEaP commands would
    accomplish this, or what is the correct protocol to follow? I'd like to avoid expanding the box size via
    larger and larger "distance" parameter in the solvateBox command.

2) How would I test if the large scale PBC breach (by a part of the solute) leads to interactions/interference
    between periodic solute images?

 Any comments or pointers to tutorials would be much appreciated.

Thank you in advance, Voytek Kasprzak

Wojciech (Voytek) Kasprzak (Contractor)
Analyst Programmer
Frederick National Laboratory for Cancer Research
Leidos Biomedical Research, Inc.
Post Office Box B
Frederick, Maryland 21702
Phone: 301-846-5537

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Received on Mon Aug 07 2017 - 09:00:03 PDT
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