Re: AMBER: if setting ntf=4, will it cause someproblem?

From: Carlos Simmerling <>
Date: Tue, 31 May 2005 11:12:30 -0400

the timestep limit is related to the frequencies of motion
in your system. these frequencies for harmonic oscillators
are related to the square root of the force constant over
the mass. So, increasing the force constant increases the
frequencies and you need smaller time steps. Ignoring the
normal angle term will not help if you still use a high
force constant in the angle restraint.

You also need to be careful of making things stiff when
calculating the PMF- depending on what you are calculating,
bond angles may change the pmf profile. For example, the
rotational barriers are affected by the angle bending terms.

Li Su wrote:
> Hi,
> I need to make my bond angles very stiff so when setting restraints I
> have to use very high force constants, but the trick is it seems to me
> the smallest timestep available is 1 fs. Therefore, I'm thinking about
> fix all angles involving hydrogen atoms for I will not need to change
> them to remove the highest frequencies in bong angle calculations. There
> is a swich "NTF" in amber, when it is set to 4, it means calculation of
> all bonds and bond angles involving H atoms will be omitted. I am
> wondering whether it will cause some problem when I am simulating PMF.
> Thanks a lot!
> Best Regards,
> Li

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Received on Tue May 31 2005 - 16:53:03 PDT
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