Hi, Fabricio
Can you send me your input files, I can do the test to check what the
problem is.
Feng
On Sun, Jun 18, 2017 at 4:47 PM, Fabrício Bracht <fabracht1.gmail.com>
wrote:
> Hi Feng Pan,
> The RMSD simulation has been crashing with the following error
>
> forrtl: info (58): format syntax error at or near *.6 ,a,f5.3 ,a,i1
> ,a)
> forrtl: severe (62): syntax error in format, unit 6, file
> /home/fabricio/enzyme/bio3d/abmd-rms/mdout.1
> Image PC Routine Line Source
> libifcore.so.5 00002AD4DA4642EB Unknown Unknown Unknown
> libifcore.so.5 00002AD4DA4CB53A Unknown Unknown Unknown
> pmemd.cuda.MPI 000000000076A08A Unknown Unknown Unknown
> pmemd.cuda.MPI 000000000071A0AA Unknown Unknown Unknown
> pmemd.cuda.MPI 00000000004E6FEC Unknown Unknown Unknown
> pmemd.cuda.MPI 000000000053DE77 Unknown Unknown Unknown
> pmemd.cuda.MPI 000000000040D29E Unknown Unknown Unknown
> libc.so.6 00002AD4DBDE0B05 Unknown Unknown Unknown
> pmemd.cuda.MPI 000000000040D1AE Unknown Unknown Unknown
>
> It runs for a while and then it crashes with this output. This does not
> come out on the mdout file, it appears in the error file from the PBS
> submission script.
> Any ideas?
>
> Thanks
> Fabrício
>
> Ps: Below are the cv.in and abmd.1.in input files.
>
> Cv.in:
> &colvar
> cv_type = 'MULTI_RMSD'
> cv_ni = 107, cv_nr = 318,
> cv_i = 4207, 4209, 4211, 4214, 4216, 4217, 4218, 4220, 4222, 4225, 4227,
> 4231, 4235, 4236, 4237, 4239, 4241, 4244, 4245, 4246, 4249, 4250, 4251,
> 4252, 4255, 4258, 4261, 4263, 4264, 4265, 4267, 4270, 4271, 4272, 4274,
> 4276, 4279, 4280, 4282, 4284, 4285, 4287, 4289, 4291, 4292, 4293, 4295,
> 4297, 4300, 4301, 4302, 4303, 4304, 0, 4207, 4209, 4211, 4214, 4216, 4217,
> 4218, 4220, 4222, 4225, 4227, 4231, 4235, 4236, 4237, 4239, 4241, 4244,
> 4245, 4246, 4249, 4250, 4251, 4252, 4255, 4258, 4261, 4263, 4264, 4265,
> 4267, 4270, 4271, 4272, 4274, 4276, 4279, 4280, 4282, 4284, 4285, 4287,
> 4289, 4291, 4292, 4293, 4295, 4297, 4300, 4301, 4302, 4303, 4304
> cv_r = 14.728, 41.301, 43.349, 13.289, 41.678, 43.093, 13.095, 43.175,
> 43.413, 13.663, 44.054, 42.393, 12.776, 41.334, 41.700, 11.586, 41.092,
> 41.558, 13.722, 41.209, 40.738, 13.342, 40.842, 39.393, 13.825, 41.872,
> 38.311, 13.129, 43.260, 38.294, 13.826, 44.340, 37.463, 11.721, 43.114,
> 37.886, 13.787, 39.463, 38.990, 14.964, 39.140, 39.267, 12.839, 38.696,
> 38.418, 13.057, 37.275, 38.084, 12.675, 36.369, 39.306, 13.253, 36.641,
> 40.704, 14.187, 36.120, 41.240, 12.709, 37.616, 41.349, 12.376, 36.877,
> 36.772, 11.331, 36.218, 36.846, 12.676, 37.505, 35.642, 13.364, 38.749,
> 35.520, 13.668, 38.812, 33.989, 12.472, 38.187, 33.400, 12.145, 36.995,
> 34.403, 12.768, 35.644, 33.959, 13.149, 34.868, 34.816, 12.877, 35.394,
> 32.660, 13.846, 34.352, 32.123, 15.231, 34.701, 32.467, 15.570, 35.865,
> 32.594, 16.031, 33.649, 32.714, 17.491, 33.765, 33.147, 18.194, 32.373,
> 33.125, 19.698, 32.433, 32.793, 20.623, 32.669, 33.881, 21.986, 32.675,
> 33.571, 22.530, 32.414, 32.305, 23.803, 32.350, 32.066, 21.650, 32.183,
> 31.255, 20.247, 32.165, 31.521, 18.277, 34.840, 32.269, 19.058, 35.575,
> 32.834, 18.061, 34.912, 30.975, 18.889, 35.704, 30.043, 19.007, 35.055,
> 28.617, 17.667, 34.554, 28.015, 17.696, 33.790, 27.021, 16.556, 34.871,
> 28.501, 18.432, 37.187, 30.009, 19.170, 38.085, 29.600, 14.700, 41.937,
> 43.919, 13.289, 42.261, 43.564, 13.045, 43.712, 43.977, 13.663, 44.600,
> 43.079, 12.785, 41.980, 42.111, 11.565, 42.130, 41.871, 13.668, 41.667,
> 41.135, 13.287, 41.288, 39.791, 14.042, 42.201, 38.771, 13.689, 43.647,
> 38.692, 14.679, 44.672, 39.270, 13.380, 44.144, 37.237, 13.569, 39.814,
> 39.465, 14.741, 39.489, 39.455, 12.529, 39.034, 39.166, 12.594, 37.573,
> 38.942, 11.964, 36.889, 40.155, 12.828, 36.750, 41.378, 14.019, 36.958,
> 41.263, 12.209, 36.762, 42.564, 11.942, 37.063, 37.634, 11.055, 36.159,
> 37.640, 12.270, 37.658, 36.460, 13.056, 38.846, 36.360, 13.579, 38.958,
> 34.972, 12.549, 38.221, 34.139, 12.086, 37.107, 35.121, 12.659, 35.670,
> 34.850, 13.208, 35.048, 35.755, 12.644, 35.268, 33.574, 13.577, 34.246,
> 33.105, 15.044, 34.778, 33.161, 15.260, 35.955, 33.083, 15.975, 33.874,
> 33.344, 17.380, 34.218, 33.739, 18.146, 32.930, 34.016, 19.572, 32.846,
> 33.602, 20.609, 33.320, 34.370, 21.974, 33.327, 33.886, 22.232, 32.878,
> 32.620, 23.496, 32.953, 32.264, 21.185, 32.463, 31.748, 19.915, 32.443,
> 32.285, 18.081, 35.117, 32.645, 19.002, 35.874, 32.991, 17.700, 35.091,
> 31.382, 18.334, 35.888, 30.432, 18.148, 35.280, 29.029, 16.711, 34.922,
> 28.575, 16.531, 35.069, 27.344, 15.888, 34.548, 29.387, 17.817, 37.379,
> 30.450, 18.463, 38.248, 29.832
>
> resolution = 0.2
> cv_min = 0.0
> cv_max = 5.0
> /
>
> abmd.1.in:
>
> &cntrl
> imin=0,
> ntx=5,
> irest=1,
> nstlim=5000000,
> dt=0.002,
> ntf=2,
> ntc=2,
> temp0=298.0,
> ntpr=1000,
> ntwx=5000,
> ntwr=5000,
> cut=12.0,
> ntb=2,
> ntp=1,
> ntt=3,
> gamma_ln=2.0,
> ig=-1, iwrap=1,
> infe = 1,
> &end
>
> &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'
>
> /
>
>
>
>
> 2017-06-16 20:41 GMT-03:00 Feng Pan <fpan3.ncsu.edu>:
>
> > 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
> > > >>
> > > >
> > > >
> > > _______________________________________________
> > > 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
Received on Sun Jun 18 2017 - 19:30:03 PDT
