Oh, ok. So I have to use AmberTools 16. I had already upgraded to
AmberTools 17. I'll recompile everything with Ambertools 16 and try it
again.
Thanks
Fabrício
2017-06-14 14:13 GMT-03:00 Feng Pan <fpan3.ncsu.edu>:
> Hi,
>
> This patch is for Amber16 and AmberTools16, so make sure you haven't
> upgraded to AmberTools17
>
> What I suggest is to make a new directory and put a fresh uncompressed
> Amber16 and AmberTools16 into it.
> Then use ./update_amber --update to update it to the latest version. (not
> ./update_amber --upgrade)
> Then ./update_amber --apply-patch=../Downloads/nfe_patch/nfe_advance.patch
> and configure, compile.
> If you need to use only the pmemd.cuda or pmemd.cuda.MPI, you can go to the
> src/pmemd and only recompile pmemd.cuda or pmemd.cuda.MPI, this saves a lot
> of time.
>
> Best
> Feng
>
> On Wed, Jun 14, 2017 at 11:47 AM, Fabrício Bracht <fabracht1.gmail.com>
> wrote:
>
> > 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
> > >
> > _______________________________________________
> > 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 - 12:00:03 PDT
