Re: [AMBER] unfolding protein and solvent density

From: Carlos Simmerling <>
Date: Tue, 17 Mar 2015 06:30:29 -0400

I'm not sure I fully understand your writing, but it sounds like you ran
NVT . If so, the density won't change. If that was a typo and you used NPT,
then your density seems lower than it should have been at the start (but
you don't say the initial value.) if the density went down, you probably
had high energies and need better minimization and equilibration. Your
protocol is simpler than what my lab uses, which involves slowly turning
off restraints the. However, it's not possible to know if that is the
problem without you looking more carefully into what happens, and when.
On Mar 17, 2015 5:32 AM, "Ibrahim Said" <> wrote:

> Dear Amber Fans
> I am running a study for the effect of guanidine hydrochloride on an enzyme
> and I built my system with packmol program and get the periodicity with
> setBox command of tleap. At the beginning of MD simulation, initial energy
> minimization was performed by applying 500 steps of steepest descent
> followed by 500 steps of conjugate gradient minimization. The protein
> atoms and the ions were kept fixed.The system was then energy minimized for
> 2500 steps of steepest descent followed by 2500 steps of conjugate gradient
> minimization using constant volume periodic boundaries. After that, a 20 ps
> molecular dynamics (MD) simulation was preformed to heat the system from 0
> K to 298 K, for which we applied the NVT ensemble. My problem is, at the
> equilibration phase to get correct density (about 1g/mm3), the system has
> 0.28 after 500ps. the cutoff range is 12A. The waterBox is 9.902x
> 9.372 x 9.602 nm^3 containing 4837 water molecules. I am running Amber12.
> Any suggestions will be appreciated. Thank you in advance.
> said
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Received on Tue Mar 17 2015 - 04:00:02 PDT
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