# Re: [AMBER] unfolding protein and solvent density

From: Ibrahim Said <saidibrahim569.gmail.com>
Date: Tue, 17 Mar 2015 12:54:10 +0200

Thanks for your prompt reply. I am sorry, there is some confusion because I
am trying to solve this problem many days ago.
My namelists for heating phase and Density equilibration phase are:

#Heating up the system

#First stage of equilibration

&cntrl

imin = 0, irest = 0, ntb = 1, ntx = 1, cut = 10, ntr = 0, ntc = 2, ntf =
2, tempi= 0.0, temp0 = 298.0, ntt = 3, gamma_ln = 1.0, ntp = 0,

nstlim = 10000, dt = 0.002, ntpr = 1000, ntwr = 1000, ntwx = 1000,

/

Keep solute fixed with weak restraint

500.0

RES 1-489

END

END

second stage

#Equilibration of whole system stage 2

&cntrl

imin = 0, ntx = 5, irest = 1, nstlim = 250000, temp0 = 298.0, tempi =
298.0, ntc = 2, ntf = 2, ntt = 3, dt = 0.002,

ntb = 2, ntp = 1, tautp = 1.0, taup = 1.0, ntwx = 1000, ntwr = 1000, ntpr =
1000, cut = 12.0, iwrap = 1, ioutfm = 1,

/

The initial density was 0.2667 while the final density is 0.2838. I do not
have any comment on these too low densities.

Thank you,

Said

On Tue, Mar 17, 2015 at 12:30 PM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:

> 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" <saidibrahim569.gmail.com> 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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> >
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Received on Tue Mar 17 2015 - 04:00:04 PDT
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