On Mon, Nov 07, 2011, hai wei wrote:
>
> I am runing a MD simulation with protein on top of Graphene sheet, During
> the simulaiton, I try to fix the graphene sheet while adding the following
> input:
>
> hold the protein fixed
> 500.0
> RES num1 num2
> END
> END
>
> While I found that the Graphene sheet does not fixed as it should be, There
> are still some ripples shown.
First, the comment indicates that you are holding the *protein* fixed, whereas
your email text indicates that you wish to keep the graphene fixed. Without
knowing anything about your system (and not knowing what num1 and num2 are),
I can't tell what should be happening.
Second, you also need to set ntr=1 in the &cntrl namelist; otherwise lines
like those above will be ignored. The output will summarize the restraints,
and tell you how many atoms were involved. If there is nothing in the about
about restrained atoms, you need to re-examine your inputs.
Third, 500 is too strong a force constant for most purposes. Consider using
a value about two orders of magnitude smaller.
...good luck....dac
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Received on Sun Nov 06 2011 - 18:30:03 PST
