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
>
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Received on Sun Jun 18 2017 - 14:00:02 PDT
