AMBER Archive (2005)

Subject: AMBER: rotational motion in periodic simulation

From: Douali, Latifa (latifa.douali_at_pnl.gov)
Date: Fri Dec 02 2005 - 12:50:28 CST

Dear all,

I am running some simulation for a piece of DNA in periodic conditions .
I am wondering if there is a way to remove the rotational motion from
periodic simulations.
In the amber8 manual, it is mentioned that NSCM is the flag to remove
the rotational and translational motion, but just from non-periodic
simulation.

I have one more question. I am doing some free energy perturbation where
I have to change both the atom type and the charges.
The problem is that Xleap gives me a warning that the unperturbed total
charge is not integral. Checking manually my perturbed and perturbed
charges, I don't notice anything wrong.
Is someone experiencing the same problem? What's the impact of this on
the future simulations?

Thank you for your advice.

Latifa
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