Apologies for the repetition, my last post wasn't answered and I'm worrying
if I am doing something wrong. Below are my previous questions:
1. Does the combination iwrap=0, ntxo=2, ioutfm=1 yield performance loss
> compared with iwrap=1, ntxo=2, ioutfm=1 ?
>
> 2. In an older post Prof Case recommended avoiding the usage of NMR-based
> restraints (nmropt=1) with iwrap=1. Does the same apply to ntr=1, iwrap=1,
> nmropt=0? A part of my protein sticks out of the unit cell although I have
> applied coordinate restraints to 20 residues (restraint_wt=200) - there's a
> slight drift to the whole protein in spite of the strong coordinate
> restraints.
>
>
I have started a protein-water simulation in a truncated octahedron using
iwrap=1, ntxo=2, ioutfm=1, but although in the .rst file (this is a
simulation restart from NVT equilibration) the protein is at the center of
the cell, in the new trajectory file the protein sticks out of the
octahedron. Is this normal?
thanks,
Thomas
--
======================================================================
Thomas Evangelidis
PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
Panepistimioupoli-Zografou
157 71 Athens
GREECE
email: tevang.pharm.uoa.gr
tevang3.gmail.com
website: https://sites.google.com/site/thomasevangelidishomepage/
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Received on Tue Feb 05 2013 - 11:30:04 PST
