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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Received on Fri Jun 16 2017 - 16:30:02 PDT
