On Sat, May 07, 2011, Kshatresh Dutta Dubey wrote:
>
> I am trying to simulate a positive charged dimeric protein. I solvated the
> system using TIP3P box and added Cl- to neutralize the system. During
> minimization, i got high positive value of EAMBER as well as other energy
> contributions which causes errors during dynamics. However, when i am not
> adding Cl- ions in system (system remains positive charge), energy of system
> is negative and dynamics runs properly. Is simulation of charged system (
> without adding Cl ions) valid?
It is valid to run without ions, but you should try to find out why you got
the problems you report.
In your message (as with many on the list posted by others) you tell us
what you *intended to do* (add ions and run minimization/dynamics), but
not what you *actually did* (the commands you ran, and important features
of the results). Without the latter information, no one will be able to
help you. Be sure you are doing things similar to the procedures shown in
the tutorials, such as the very first one.
...dac
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Received on Sat May 07 2011 - 06:30:03 PDT
