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
--
========================================
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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