Re: [AMBER] SMD and free energy value

From: bharat gupta <>
Date: Thu, 21 Jul 2016 23:20:47 +0900

Dear Amber Users,

I am performing a SMD simulation for an enzyme reaction with three steps
happening in a concerted manner. Though I was able to achieve the three
steps but the energy barrier for all the three steps is around 60 kcal/mol.
What could be the reason for such a high energy? I was suggested previously
to perform SMD for a single step first and lower the harm value. Since I am
following this paper where all the three steps were performed in a single
SMD simulation (,
I cannot perform SMD for invidual steps, as this will not solve my purpose.
So, I tried to lower the harm value and performed the simulation again,
then in this case, I was not able to see all three steps occurring

I would highly appreciate if somebody could tell how can I get a reasonable
energy barrier for all the three steps?

*Best Regards*
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Received on Thu Jul 21 2016 - 07:30:02 PDT
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