Hi, Fabricio
First, don't forget to set the cv_min and cv_max,
As I understand, since you set the same group of atoms twice, the value of
CV should be sqrt(0.5*R1^2+0.5*R2^2).
Ideally you should get two minima along this CV, but it could also be
possible that the positions of the two minima
are too close to be distinguished. I still suggest you to try this first to
see what the result looks like. If it is not good,
you can change to two-dimensional CVs.
And nscm should not affect ABMD, you can set it or just leave it as
default.
Feng
On Fri, Jun 16, 2017 at 7:05 PM, Fabrício Bracht <fabracht1.gmail.com>
wrote:
> Hi Feng Pan. I'm trying out the MULTI_RMSD cv type in order to see if I can
> get the relative free energy from two different conformations of the loop.
> I just wanted to check with you if the following input will give me what I
> want.
> &colvar
> cv_type = 'MULTI_RMSD'
> cv_ni = 107, cv_nr = 318,
> cv_i = "Here I listed all heavy atoms in the loop, followed by a 0 and
> then followed by the same list again"
> cv_r = "Here I listed the xyz coordinates of the first conformation
> followed by the xyz coordinates of the second conformation"
> resolution = 0.2
> /
>
> Is this the correct way to list the two conformations I want as reference?
>
> Also, Is it necessary to set the nscm flag in the input script?
>
> Thank you
>
> Fabrício
>
>
> 2017-06-14 15:36 GMT-03:00 Fabrício Bracht <fabracht1.gmail.com>:
>
> > 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_Unapplie
> >> d_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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--
Feng Pan
Ph.D. Candidate
North Carolina State University
Department of Physics
Email: fpan3.ncsu.edu
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Received on Fri Jun 16 2017 - 17:00:03 PDT
