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
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Received on Wed Jun 14 2017 - 10:30:02 PDT
