[gmx-users] i don't know how can i determine emtol

[Justin Lemkul]

On 11/20/12 3:38 PM, Ali Alizadeh wrote:
> Dear Justin
>
> I am using MD instead of steep, and i have a problem, I do not know
> value of emtol so that energy of system reaches to -51 kj/mol, i
> determine it then run it but it reaches to -30 kj/mol(only for 1ns)
>
> original results :
>
>   http://alichemical.persiangig.com/document/11.jpg
>

The value of emtol is only relevant in EM and has no relationship whatsoever to 
MD.  In fact, this keyword is ignored if an EM algorithm is not chosen as the 
integrator.

No one can help you if you don't fully describe what you're doing.  That appears 
to be a figure from some paper - what's going on?  If it is from a paper, what 
were the methods?  How was the plot produced?  Otherwise no one will have any 
idea what's going on.  You can't just force a system to adopt some series of 
configurations that yield a given potential energy.

Please describe in full what you are doing, and provide answers to all the 
questions posed above, or else I'm afraid I'm not going to have anything else 
useful to say.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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