[gmx-users] Re:Question regarding Gromacs
lucioric at ibt.unam.mx
Mon Sep 29 19:30:32 CEST 2008
If you are doing simulated annealing, your system explode if you are heating
all the system (protein and water). Divide your system in protein and water
and heat only the protein.
From: "Tsjerk Wassenaar" <tsjerkw at gmail.com>
Sent: Monday, September 29, 2008 2:50 AM
To: "minnale" <minnale_gnos at rediffmail.com>; "Discussion list for GROMACS
users" <gmx-users at gromacs.org>
Subject: Re: [gmx-users] Re:Question regarding Gromacs
>> Thanks for the reply, what may be the reason GROMACS became great?
> Check the JCC 2005 paper: http://www.ncbi.nlm.nih.gov/pubmed/16211538
>> sometimes though system explodes it will generate energy minimisation
>> output.gro file we cant use this file for further run?
> Need more information..., what did you try to do? Did you do EM? Check
> for overlaps, go through your system carefully, don't stick your head
> in the sand and continue the simulation. Mind you that MD programs
> adhere to the Rubbish-in Rubbish-out protocol (RRP :p).
> Tsjerk A. Wassenaar, Ph.D.
> Junior UD (post-doc)
> Biomolecular NMR, Bijvoet Center
> Utrecht University
> Padualaan 8
> 3584 CH Utrecht
> The Netherlands
> P: +31-30-2539931
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