[gmx-users] Re:Question regarding Gromacs

[Lucio Montero]

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

> Minnale,
>
>> 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).
>
> Cheers,
>
> Tsjerk
>
> -- 
> 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
> F: +31-30-2537623
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