AMBER Archive (2009)

Subject: [AMBER] Re:Etot positive

From: Jio M (jiomm_at_yahoo.com)
Date: Mon Nov 16 2009 - 22:59:26 CST

Thanks to Dr. Ross and Dr. Carlos for replies and suggestions

>it's not possible to say since we don't know what you are simulating. if

>this were a solute in water I would say there is probably something wrong.

I built macromolecule ( ~1300 atoms) using residues (RESP charged and
gaff parametrised individual residues) and then annealed it

Macromolecule was then solvated in dichloromethane (dcm) using single
molecule of dcm ( also RESP charged and H2-C-Cl missing parameter was
provided with frcmod file), which added ~780 dcm molecules to one
macromolecule. this all was minimised ,heated (0-300K) and equilibrated
( at 300K NTP)

the Etot finally in output file is Positive..... which creates doubt
regarding my procedure that I have adopted right from the first step.
Dr. Ross has also suggested

 

> you need to look at relative energy differences, magnitudes of fluctuations etc.

your suggestions will prove very helpful to me

thanks and regards;

JIomm

##################################

> 1) Is it necessary that Etot should be negative .... I have seen in

> most of the querries and tutorial output, that Etot is negative.

#There is no requirement for the total energy, or the potential energy to be

#negative. The energy origin is actually somewhat arbitrary in molecular
#dynamics simulations so individual energy values do not tell you much, you

#need to look at relative energy differences, magnitudes of fluctuations etc.

#All the best

#Ross

      
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