[AMBER] unfolding protein and solvent density

From: Ibrahim Said <saidibrahim569.gmail.com>
Date: Tue, 17 Mar 2015 11:32:03 +0200

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.

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Received on Tue Mar 17 2015 - 03:00:02 PDT
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