From: Yaxin An (yxan2016_at_gmail.com)
Date: Fri Dec 08 2017 - 09:06:19 CST
Hi Josh;
Sorry I did not describe clearly.
The PBC was 40by40by100. That meant I used 100 A in the z-direction. I pull
the alkane molecule out along the Z direction.
I also saw most people used TI to calculate the free energy of hydration. I
may change to the TI or FEP method.
Thanks a lot.
Yaxin
On Fri, Dec 8, 2017 at 2:07 AM, namd-l digest <
owner-namd-l-digest_at_ks.uiuc.edu> wrote:
>
> namd-l digest Friday, December 8 2017 Volume 01 : Number 2316
>
>
>
> In this issue:
>
> namd-l: Free energy did not converge by using ABF
> namd-l: metadynamics run in NAMD or using plumed in NAMD
> Re: namd-l: metadynamics run in NAMD or using plumed in NAMD
> Re: namd-l: Free energy did not converge by using ABF
>
> ----------------------------------------------------------------------
>
> Date: Thu, 7 Dec 2017 18:22:31 -0500
> From: Yaxin An <yxan2016_at_gmail.com>
> Subject: namd-l: Free energy did not converge by using ABF
>
> Hi All:
>
> I am running ABF simulations for the free energy of hydration of alkanes.
> But I got different values for the free energies every time when I repeat
> the simulations, like 1.5 and 3.0 Kcal/mol.
>
> In the simulation, there was one water box (40 Angstrom by40 by 40). The
> reaction coordinate is the Z distance between COM of the water box and the
> one alkane molecule. The reaction coordinate spans from 0 to 45.
>
> I split the reaction coordinate into 9 windows: 0-5, 5-10, ....,40-45. And
> I ran the simulation in each window for 50 ns. Each time the free energy
> converged. But when I repeated it, the free energy converged to a different
> value.
>
> Hope someone can give me some suggestion.
>
> Thanks
> Yaxin
>
> ------------------------------
>
> Date: Thu, 7 Dec 2017 17:49:22 -0600
> From: Rabeta Yeasmin <rabetayeasmin_at_gmail.com>
> Subject: namd-l: metadynamics run in NAMD or using plumed in NAMD
>
> Dear NAMD users,
>
> I am trying to run metadynamics in NAMD. I have searched online for related
> information. I have found one tutorial in NAMD tutorial and also found
> something like-running metadynamics using plumed version- in NAMD version-.
> I am wondering if these two methods are same or not. If yes, how am I going
> to use plumed with NAMD.
>
> Thanks.
>
> Rabeta Yeasmin
>
> ------------------------------
>
> Date: Fri, 8 Dec 2017 09:22:06 +0800
> From: yjcoshc <yjcoshc_at_gmail.com>
> Subject: Re: namd-l: metadynamics run in NAMD or using plumed in NAMD
>
> Hi, plumed only officially support NAMD 2.9. For later version I have
> post a patch in plumed user group:
>
> https://groups.google.com/d/msg/plumed-users/xcfXPpm1HiE/tBmwRN3aAwAJ
>
> However I suggest running metadynamics in NAMD with its colvars module.
> Both metadynamics algorithms in colvars and plumed are actually the
> same, but their implementations may differ. The difference includes
> energy units, SIGMA(plumed) vs hillWidth(colvars) and so on.
>
>
> e ( 2017e9412f 08f % 07:49, Rabeta Yeasmin e i :
> > Dear NAMD users,
> >
> > I am trying to run metadynamics in NAMD. I have searchedB online for
> > related information. I have found one tutorial in NAMD tutorial and
> > also found something like-running metadynamics using plumed version-
> > in NAMD version-. I am wonderingB if these two methods are same or not.
> > If yes, how am I going to use plumed with NAMD.
> >
> > Thanks.
> >
> > Rabeta Yeasmin
>
> ------------------------------
>
> Date: Fri, 8 Dec 2017 01:23:53 +0000
> From: "Vermaas, Joshua" <Joshua.Vermaas_at_nrel.gov>
> Subject: Re: namd-l: Free energy did not converge by using ABF
>
> Hi Yaxin,
>
> I'm super confused. A water "box" suggests that you have periodic
> boundary conditions. How can your alkane molecule move out of water this
> way? Wouldn't a value of 45 imply that you are really at -5 and
> re-entering the waterbox from the bottom? This should be really obvious
> if you visualize a water surface, as I'd expect a hole in the water
> surface on the "bottom" that matches where the alkane is on the top.
> Normally I see this done using FEP or TI rather than a pulling
> technique, since then PBC makes perfect sense and you don't need to pull
> your molecule into a vacuum.
>
> - -Josh
>
> On 12/07/2017 04:28 PM, Yaxin An wrote:
> > Hi All:
> >
> > I am running ABF simulations for the free energy of hydration of
> > alkanes. But I got different values for the free energies every time
> > when I repeat the simulations, like 1.5 and 3.0 Kcal/mol.
> >
> > In the simulation, there was one water box (40 Angstrom by40 by 40).
> > The reaction coordinate is the Z distance between COM of the water box
> > and the one alkane molecule. The reaction coordinate spans from 0 to 45.
> >
> > I split the reaction coordinate into 9 windows: 0-5, 5-10, ....,40-45.
> > And I ran the simulation in each window for 50 ns. Each time the free
> > energy converged. But when I repeated it, the free energy converged to
> > a different value.
> >
> > Hope someone can give me some suggestion.
> >
> > Thanks
> > Yaxin
> >
> >
> >
>
> ------------------------------
>
> End of namd-l digest V1 #2316
> *****************************
>
>
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