On Mon, Feb 23, 2015, Fatemeh Sadat Alavi wrote:
>
> I compared the starting structure and the minimized structure. I can see the
> the structure has changed slightly, and I think that there are no major
> problem.
Have you used "check" command in cpptraj to look for bad contacts?
> If I don't have good minimized structure, What do I do?
Minimize for more steps? What is the RMS of the force vector at the end of
the minimization?
>
> As I said before, I calculated MD (heating) with ntwx=1 ntpr=1 ntslim=100 ,I
> saw heat.mdcrd and complex_solvated.prmtop files by chimera software!
I'm not sure what this last sentence means. Do you still get the vlimit
error? Is it still at the first MD step?
...dac
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Received on Mon Feb 23 2015 - 06:00:08 PST
