Hello Feng Pan. Thank you for the fast reply.
I've downloaded the patch but the patching procedure failed. Maybe its
something I did.
Before applying the patch, I've updated amber16 and recompiled to make sure
I had the latest version.
After that, I did
cd $AMBERHOME
./update_amber --apply-patch=../Downloads/nfe_patch/nfe_advance.patch
The ouput is:
Preparing to apply a third-party update/patch... please wait.
Applying nfe_advance.patch
PatchingError: .patches/ThirdParty16_Unapplied_Patches/nfe_advance.patch
failed to apply. No changes made from this patch
Any suggestions?
Thanks
Fabrício
2017-06-13 18:48 GMT-03:00 Feng Pan <fpan3.ncsu.edu>:
> Hello,
>
> Here, the cv_min and cv_max are only to set the range of output biasing
> potential, not the range of
> sampling. To restrain the CV in the sample, you should add another &pmd
> module. like
> For Amber16, if you are using GPU, you should apply this patch first and
> then you can use &pmd in GPU
> http://ambermd.org/tutorials/advanced/tutorial31/nfe_advance.patch.tar.gz
> There is README file and also you can check the new Amber 2017 manual for
> the usage of &pmd.
>
> For wt_bias_1.nc and wt_bias_2.nc, they are the same, so choosing either
> of
> them is OK.
>
> For the selection_constant, this is the original paper of this idea
> http://pubs.acs.org/doi/abs/10.1021/ct900524t
> Here the constant is from the equation and is associated with the selection
> time period and
> density of CV. I also check the paper and it is hard to find a practical
> way to choose the constant.
> Actually the selection algorithm is to enhanced the sampling and not always
> necessary to apply,
> often if the sampling rate is not so slow you can leave out the selection
> algorithm.
> Here two replicas are too few for selection, if you want to use selection I
> suggest at least 4 replicas
> should be used.
>
> Best
> Feng Pan
>
> On Tue, Jun 13, 2017 at 4:55 PM, Fabrício Bracht <fabracht1.gmail.com>
> wrote:
>
> > Dear All,
> > I've simulated a protein in order to back up some experimental data
> > regarding the importance of a Tyr residue. This residue is part of a loop
> > that has an open/close type motion. The study began because the
> difraction
> > structure showed that this Tyr is quite different from other structures
> > known in the literature. With MD we have been able to see that this Tyr
> > residue does something close to a pendulum motion. It prefers some
> > configurations over others, meaning, it prefers either to be facing the
> > catalytic center or it prefers to face the opposite way. This hinge
> motion
> > is associated with changes in the loop conformation and it seems that the
> > outward/inward positions are related to the phi/psi dihedral angles of
> this
> > particular residue (or a neighboring residue, we are still not sure).
> I've
> > worked with umbrella sampling before in amber, but I would like to use
> the
> > abmd suite to calculate the relative free energy differences between
> these
> > two configurations.
> > I've started following TUTORIAL A31, specifically part 1 (Calculating 2-d
> > free energy landscapes for a di-alanine peptide), but I am having some
> > trouble figuring out some things.
> > First, as a test run, I've adapted the files from the tutorial in order
> to
> > describe the two TORSIONS I would like to sample. The mdin abmd variables
> > are set as:
> >
> > &abmd
> >
> > mode = 'FLOODING'
> >
> > timescale = 1.0
> > monitor_freq = 500
> > monitor_file = 'abmd_monitor_1.dat'
> > cv_file = 'cv.in'
> > umbrella_file = 'bias_1.nc'
> >
> > selection_freq = 5000
> > selection_constant = 0.00001
> > selection_epsilon = 0.0
> > wt_temperature = 10000
> > wt_umbrella_file = 'wt_bias_1.nc'
> >
> > And the collective variable file 'cv.in' is:
> >
> > &colvar
> > cv_type = 'TORSION'
> > cv_ni = 4
> > cv_i = 4270,4272,4274,4291 !phi
> > resolution = 0.2
> > cv_min = -1.40
> > cv_max = 1.40
> > /
> >
> > &colvar
> > cv_type = 'TORSION'
> > cv_ni = 4
> > cv_i = 4291,4272,4274,4303 !psi
> > resolution = 0.2
> > cv_min = -0.7
> > cv_max = 0.7
> > /
> >
> > There are some things I would like to ask though. First, I've used the
> > cv_min and cv_max to specify that I would only like to sample torsion
> > values that ranges from the maximum and minimum values I observed in the
> MD
> > simulation. Is that necessary, or even good practice?
> > For this test, I am running only 2 replicas. From the tutorial, I could
> see
> > that the wt_bias_#.nc files are equal (I've used cmp wt_bias_1.nc
> > wt_bias_2.nc). So, it would not matter which file I choose for post
> > processing with nfe-umbrella-slice, correct?
> > The manual states that choosing the best selection_constant is somewhat
> of
> > an art form. Can you suggest some literature (or point it out explicitly)
> > as to how I would choose the best values for my simulations?
> >
> > Thank you
> > Fabrício Bracht
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Feng Pan
> Ph.D. Candidate
> North Carolina State University
> Department of Physics
> Email: fpan3.ncsu.edu
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Jun 14 2017 - 09:00:02 PDT
