[gmx-users] gromacs.org_gmx-users Digest, Vol 142, Issue 42
Mehreen Jan
mehreen_jan1990 at yahoo.com
Tue Feb 9 10:44:05 CET 2016
Subject: Fw: wrong number of control atomes in
> hdb
> >
> > > > respected sir!
> > > > thank you for advise
> > > >
> > > > thank you sir for advise i just copy folder
> 43A1p
> > and
> > > past
> > > > in top file and in GMXLIB and it work error
> is
> > solved
> > > know
> > > > after running the command:
> > > > pdb2gmx -f protein.top -o protein.gro
> > > > select the forcefield 43A1p the following
> error
> > is
> > > occurs
> > > > i google it but i can't get it exactly and i
> read
> > > manual but
> > > > difficult to understand because of no
> experience
> > .
> > > > respected sir kiendle find the attachment .
> > > >
> > > >
> > > > error in hdb file
> ./gromacs43A1p/aminoacid.hdb:
> > > >
> > > > wrong number of control atoms (2 iso3) on
> line:
> > > > 2 3 N -C -CA
--------------------------------------------
On Tue, 9/2/16, gromacs.org_gmx-users-request at maillist.sys.kth.se <gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:
Subject: gromacs.org_gmx-users Digest, Vol 142, Issue 42
To: gromacs.org_gmx-users at maillist.sys.kth.se
Received: Tuesday, 9 February, 2016, 1:20 PM
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Today's Topics:
1. Different results for same protein's
simulation in 4.6.5 and
5.0.4 (SAPNA BORAH)
2. Re: Different results for same
protein's simulation in 4.6.5
and 5.0.4 (Mark Abraham)
3. Re: creating representative structures
(Mark Abraham)
4. Re: pp/pme ratio differences between
gromacs 5.0.x and 5.1.x
(Mark Abraham)
5. Re: Fwd: FW: PME settings in free
energy calculations
(Mark Abraham)
----------------------------------------------------------------------
Message: 1
Date: Tue, 9 Feb 2016 12:52:41 +0530
From: SAPNA BORAH <sapnauser365 at gmail.com>
To: gmx-users at gromacs.org
Subject: [gmx-users] Different results for same protein's
simulation
in 4.6.5 and 5.0.4
Message-ID:
<CAEL2Jf7tNT94MnMbW3h6YnsKL63tC0+xeZQhMFnre7WVpngVCQ at mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
Dear all,
I have tried running the same protein in the two versions of
gromacs 4.6.5
and 5.0.4. Now, both the runs are producing entirely
different results.
The results till equilibration are same.
After the run however, there is a total change in the
production results. I
have used the same mdp files.
I have rerun the systems and they still produce similar
results in the same
version.
The protein structure is a modelled one.
Thanks in advance.
Sapna.
Sapna Mayuri Borah
c/o Dr. A. N. Jha
Research student
Tezpur University,
India
------------------------------
Message: 2
Date: Tue, 09 Feb 2016 07:37:54 +0000
From: Mark Abraham <mark.j.abraham at gmail.com>
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Different results for same
protein's
simulation in 4.6.5 and 5.0.4
Message-ID:
<CAMNuMARf1tJD+thVQvoSuN9SPkYhW06Oo2w6=bbFh6UdvFsyYw at mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
Hi,
This is quite normal.
http://www.gromacs.org/Documentation/Terminology/Reproducibility.
You
should see a similar range of variation in the trajectories
produced in the
two versions that are incompletely sampling the same
ensemble, but one can
say very little about two single observed trajectories
sampled from them.
Mark
On Tue, Feb 9, 2016 at 8:23 AM SAPNA BORAH <sapnauser365 at gmail.com>
wrote:
> Dear all,
>
> I have tried running the same protein in the two
versions of gromacs 4.6.5
> and 5.0.4. Now, both the runs are producing entirely
different results.
>
> The results till equilibration are same.
>
> After the run however, there is a total change in the
production results. I
> have used the same mdp files.
>
> I have rerun the systems and they still produce similar
results in the same
> version.
>
> The protein structure is a modelled one.
>
>
> Thanks in advance.
> Sapna.
>
> Sapna Mayuri Borah
> c/o Dr. A. N. Jha
> Research student
> Tezpur University,
> India
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List
before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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or
> send a mail to gmx-users-request at gromacs.org.
>
------------------------------
Message: 3
Date: Tue, 09 Feb 2016 07:46:31 +0000
From: Mark Abraham <mark.j.abraham at gmail.com>
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] creating representative structures
Message-ID:
<CAMNuMAQgBnhazSinyeDzpLdwEZDuNSbDmZ77bLJhO5qkt7w06g at mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
Hi,
On Mon, Feb 8, 2016 at 6:24 PM Shyno Mathew <sm3334 at columbia.edu>
wrote:
> Dear all,
>
>
> I have few questions regarding creating representative
structures. For
> simplicity, let?s say I have a trajectory of 5 frames:
>
> 1. g_rmsf: After reading
previous posts, here is what I understood.
> The average structures calculated using g_rmsf (by
specifying ?ox) is
> literally the average of x, y, z co-ordinates of each
atom over all the 5
> frames in my case. Energy minimizing this averaged
structure might give a
> meaningful structure?
>
It'll give a structure that conforms to chemical
expectations, but the
"meaning" of any plausible candidate for an "average"
structure is doubtful
at best. If there is a group of microstates that share
structural
similarity, it does not follow that RMSD will identify it,
nor that
averaging of coordinates will produce a meaningful average.
What is the RMS
average position of a set of balls being juggled?
> 2. g_cluster: Here I am
using the gromos method. I read the reference
> paper (Daura et al.). Using gromos method and by just
specifying ?cl (not
> ?av) I get the middle structures for each cluster.
Let?s say I get 2
> clusters using rmsd 0.16. Now the representative
structures of these two
> clusters (obtained in the out.pdb) should exactly
correspond to two frames
> in my original trajectory (the one with 5 frames)?
>
I don't know, but you should try it and see. Make a
trajectory of a water
molecule as PDB with a few frames and play with editing the
coordinates by
hand and passing them to g_cluster until you are happy you
understand how
it works.
> 3. My final question is
regarding how exactly g_cluster works, here
> is what I understand from Daura et al.
>
> If I use g_cluster with gromos method, the code will
look for neighbors of
> each frame within specified cutoff.
>
> Assume the first time the code finds the following:
>
> frame 0 has two neighbors: frames 2,3 within
cutoff
>
> frame 1 has three neighbors: frames 2, 3, 4 within
cutoff
>
> frame 2 has four neighbors: frames 0, 1, 3, 4 within
cutoff
>
> frame 3 has three neighbors: frames 0,1, 2 within
cutoff
>
> frame 4 has two neighbors: frames 1,2 within cutoff
>
>
>
> Since frame 2 has the highest number of neighbors, it's
considered the
> center cluster and this frame along with neighbors are
removed. The same
> calculation is performed on the remaining frames if I
had more frames.
>
No idea, but again try it and see.
Mark
> Thanks in advance for your help,
>
> Sincerely,
>
> Shyno
>
> --
> Shyno Mathew
> PhD Candidate
> Department of Chemical Engineering
> Graduate Assistant
> Office of Graduate Student Affairs
> The Fu Foundation School Of Engineering and Applied
Science
> Columbia University
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List
before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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> send a mail to gmx-users-request at gromacs.org.
------------------------------
Message: 4
Date: Tue, 09 Feb 2016 07:59:18 +0000
From: Mark Abraham <mark.j.abraham at gmail.com>
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] pp/pme ratio differences between
gromacs
5.0.x and 5.1.x
Message-ID:
<CAMNuMAReBaEYCG6fok-3MG5w0p4NUWats93xQvY6ge3ngPpNhw at mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
Hi,
On Sun, Feb 7, 2016 at 8:00 PM Johannes Wagner <johannes.wagner at h-its.org>
wrote:
> hey guys,
> came across an issue with pp/pme ratio difference from
5.0 to 5.1. For a
> system running on 2 nodes with a pp/pme ratio of 80:16
on 5.0, the same
> thing starts with 72:24 on gromacs 5.1. The 5.1 run has
a much higher load
> imbalance and is hence slower. Are there known changes
from 5.0 to 5.1 in
> the pp/pme ratio that cause this?
>
Yes and no. Even on only two nodes, your observations can be
affected by
network congestion, so I would investigate whether you can
reproduce the
observations. The changes that I identified that had the
capacity to change
performance are noted at
http://manual.gromacs.org/documentation/5.1/ReleaseNotes/performance.html.
For example, if you're using LINCS then the SIMD
improvements there affect
only the PP ranks so it might seem to the auto-tuner that
it's more
efficient to use fewer PP ranks. Then later some kind of
load imbalance has
a stronger effect. The interactions of DD DLB and PME tuning
are complex,
and we can't rule out that there's a problem that we should
fix. But we
can't say much without being able to compare some
(reproducible) log files.
Mark
cheers, johannes
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List
before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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or
> send a mail to gmx-users-request at gromacs.org.
>
------------------------------
Message: 5
Date: Tue, 09 Feb 2016 08:20:17 +0000
From: Mark Abraham <mark.j.abraham at gmail.com>
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Fwd: FW: PME settings in free
energy
calculations
Message-ID:
<CAMNuMAQ9oJbDrAuW9danqaXXmhTNw=zsJXZ9S-tDw9WaRsrsgg at mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
Hi,
On Fri, Feb 5, 2016 at 1:32 PM Dries Van Rompaey <dries.vanrompaey at gmail.com>
wrote:
> Hi,
>
> The corresponding mdp output section is:
>
> ; OPTIONS FOR ELECTROSTATICS AND VDW
> ; Method for doing electrostatics
> coulombtype
= PME
> coulomb-modifier
= Potential-shift-Verlet
> rcoulomb-switch = 0
> rcoulomb
= 1.0
> ; Relative dielectric constant for the medium and the
reaction field
> epsilon-r
= 1
> epsilon-rf
= 0
> ; Method for doing Van der Waals
> vdwtype
= cutoff
> vdw-modifier
= Potential-switch
> ; cut-off lengths
> rvdw-switch
= 0.9
> rvdw
= 1.0
> ; Apply long range dispersion corrections for Energy
and Pressure
> DispCorr
= EnerPres
> ; Extension of the potential lookup tables beyond the
cut-off
> table-extension = 1
> ; Separate tables between energy group pairs
> energygrp-table =
> ; Spacing for the PME/PPPM FFT grid
> fourierspacing
= 0.08
> ; FFT grid size, when a value is 0 fourierspacing will
be used
> fourier-nx
= 0
> fourier-ny
= 0
> fourier-nz
= 0
> ; EWALD/PME/PPPM parameters
> pme_order
= 6
> ewald_rtol
= 1e-06
> ewald-rtol-lj
= 0.001
> lj-pme-comb-rule
= Geometric
> ewald-geometry
= 3d
> epsilon_surface = 0
That all seems reasonable.
> I evaluated the energy with:
>
> Verlet - settings above (with standard
verlet-buffer-tolerance)
> @ s0 legend "Coulomb-14"
> @ s1 legend "Coulomb (SR)"
> @ s2 legend "Coul. recip."
> 0.000000
-2221.295898 -546205.250000 9271.518555
> Total - 539155.0273
>
> Verlet - settings above - with verlet-buffer-tolerance
-1
> 0.000000
-2221.295898 -546205.250000 9271.516602
> Total -539155.029296
>
That kind of agreement is expected, but perhaps might agree
exactly if you
were following
http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy
Group - settings above
> @ s0 legend "Coulomb-14"
> @ s1 legend "Coulomb (SR)"
> @ s2 legend "Coul. recip."
> 0.000000
-2221.296387 -487993.593750 -48931.437500
> Total -539146.3276
>
The difference in those components is expected - in PME you
have to avoid
counting contributions in the long-range part from pairs
that are excluded
e.g. from the bonded topology. The two schemes handle this
in different
places. Their sum should match (within the limits of
floating-point
arithmetic), and a relative error under 1e-5 for summing a
few million
numbers is acceptable for judging the equivalence of the
implementations.
Verlet - 3 nm cutoffs, 2.9 vdwswitch, coulomb-modifier none
> @ s0 legend "Coulomb-14"
> @ s1 legend "Coulomb (SR)"
> 0.000000
-2221.295898 -774817.875000
> Total -777039.1709
>
>
> Group - 3 nm cutoffs, 2.9 vdwswitch, coulomb-modifier
none
> @ s0 legend "Coulomb-14"
> @ s1 legend "Coulomb (SR)"
> 0.000000
-2221.296387 -553398.125000
> Total -555619.4214
>
That ought to agree much better, but It's hard to speculate
on where the
problem lies without seeing log files. Please upload some to
a file sharing
service and post the links here (list doesn't take
attachments)
Mark
> Thanks,
>
> Dries
>
> On 4 February 2016 at 14:48, Michael Shirts <mrshirts at gmail.com>
wrote:
>
> > Also, can you be more precise about the
inconsistency in the outputs
> > you are seeing (with numerical output from GROMACS
and analysis code).
> >
> > On Thu, Feb 4, 2016 at 6:17 AM, Michael Shirts
<mrshirts at gmail.com>
> wrote:
> > > Hi, Dries-
> > >
> > > Can you print out what the corresponding
section of mdout.mdp look
> like?
> > >
> > > Have you tried using the cutoffs above
with group cutoffs, and seen
> > > what the difference is?
> > >
> > > On Thu, Feb 4, 2016 at 4:59 AM, Dries Van
Rompaey
> > > <dries.vanrompaey at gmail.com>
wrote:
> > >> Hi,
> > >>
> > >> I'm using PME with the default
Potential-Shift-Verlet modifier. If I'm
> > >> interpreting the manual and comments on
the mailinglist correctly, the
> > >> settings for rcoulomb-switch shouldn't
affect this and PME-switching
> > >> shouldn't be necessary (although there
seems to have been some
> > discussion
> > >> about this, https://gerrit.gromacs.org/#/c/2220/). Has a consensus
> been
> > >> reached elsewhere?
> > >>
> > >> Current nonbonded settings in my .mdp
files are:
> > >> ; Electrostatics
> > >> coulombtype
= PME
> > >> rcoulomb
= 1.0
> > >>
> > >> ; van der Waals
> > >> vdwtype
= cutoff
> > >> vdw-modifier
= Potential-switch
> > >> rvdw-switch
= 0.9
> > >> rvdw
= 1.0
> > >>
> > >> ; Apply long range dispersion corrections
for Energy and Pressure
> > >> DispCorr
= EnerPres
> > >>
> > >> ; Spacing for the PME/PPPM FFT grid
> > >> fourierspacing
= 0.08
> > >>
> > >> ; EWALD/PME/PPPM parameters
> > >> pme_order
= 6
> > >> ewald_rtol
= 1e-06
> > >> epsilon_surface
= 0
> > >>
> > >> Thanks in advance,
> > >>
> > >> Dries
> > >>
> > >> On 4 February 2016 at 00:56, Michael
Shirts <mrshirts at gmail.com>
> wrote:
> > >>
> > >>> Hi, Dries-
> > >>>
> > >>> Questions like this are probably best
answered on the gmx-users list.
> > >>> I can't say too much for the Verlet
scheme -- I know that it was
> > >>> relatively recently adapted for free
energies, and there may be some
> > >>> combinations of settings that could
give unanticipated results.
> > >>>
> > >>> Pretty much all of our experience
about nonbonded calculations and
> > >>> free energies is collected in the
following paper:
> > >>> http://pubs.acs.org/doi/abs/10.1021/ct4005068. We used
the group
> > >>> cutoff scheme since that was the only
one that was supported in
> > >>> GROMACS at the time.
> > >>>
> > >>> Since you haven't sent any files,
it's hard to tell what is actually
> > >>> going on. The one thing that has a
tendency to happen with the more
> > >>> recent update schemes is if you set a
potential modifier that is a
> > >>> switch, but don't set the distance
the switch starts at, then it is
> > >>> automatically set to zero.
Check the mdout.mdp to see if this is
> > >>> happening.
> > >>>
> > >>> > From: Van Rompaey Dries <Dries.VanRompaey at uantwerpen.be>
> > >>> Date: Wednesday, February 3, 2016 at
12:34 PM
> > >>> To: Michael Shirts <michael.shirts at colorado.edu>
> > >>> Subject: PME settings in free energy
calculations
> > >>>
> > >>> Dear prof. Shirts,
> > >>>
> > >>> I'm currently trying to figure out
the PME settings for a relative
> > >>> free binding energy simulation I'm
working on. I took the parameters
> > >>> from Matteo Aldeghi's
> > >>> paper(
> > >>>
> >
> http://pubs.rsc.org/en/content/articlelanding/2015/sc/c5sc02678d#!divAbstract
> > >>> )
> > >>> as a starting point (adapted for the
Verlet scheme by scaling the
> > >>> fourierspacing to 0.08 and setting
coulomb = rvdw = 1.0). I then
> tried
> > >>> to verify these settings by comparing
a single point energy
> > >>> calculation with these settings and
one with very long coulomb
> cutoffs
> > >>> as recommended on alchemistry.org.
> > >>>
> > >>> Unfortunately, I can't seem to get
this quite right. I'm getting
> > >>> differences in the hundreds of
kj/mol, leading me to suspect I'm
> doing
> > >>> something wrong. I'm calculating the
energy values by extracting
> > >>> CoulombSR and Coul-recip from the
energy.xvg files. I've tried
> > >>> calculating the energy with coulomb
cutoffs at 3 nm and 10 nm, but
> > >>> agreement with the PME results
remains rather poor. David Mobley
> > >>> mentioned you performed extensive
research on this topic, and I'm
> > >>> hoping you could point me in the
right direction.
> > >>>
> > >>> Thanks in advance,
> > >>>
> > >>> Dries
> > >>>
> > >>>
> > >>>
> > >>> ~~~~~~~~~~~~~~~~
> > >>> Michael Shirts
> > >>> Associate Professor
> > >>> michael.shirts at colorado.edu
> > >>> Phone: (303) 735-7860
> > >>> Office: JSCBB D317
> > >>> Department of Chemical and Biological
Engineering
> > >>> University of Colorado Boulder
> > >>> --
> > >>> Gromacs Users mailing list
> > >>>
> > >>> * Please search the archive at
> > >>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List
before
> > >>> posting!
> > >>>
> > >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >>>
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> > >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or
> > >>> send a mail to gmx-users-request at gromacs.org.
> > >>>
> > >> --
> > >> Gromacs Users mailing list
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> > posting!
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