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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Received on Mon Nov 16 2009 - 21:30:02 PST
