[gmx-users] Re: Cylinder Pulling output file pullx.xvg wrong

Kun Huang harryhuangkun at gmail.com
Sat Apr 23 19:18:58 CEST 2011


Dear Chris:

Thanks for you reply. You are right. The printf in gromacs 4.0.7 is very
different from gromacs 4.5.3. and the output file in gromacs 4.5.3 is right.
I think they fixed the bug :)

Thank you very much,
Kun

On Mon, Apr 18, 2011 at 1:41 PM, <gmx-users-request at gromacs.org> wrote:

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> Today's Topics:
>
>   1. Re: Re: energy group exclusions (Justin A. Lemkul)
>   2. Re: diverging temperature with pressure coupling (Dommert Florian)
>   3. Cylinder Pulling output file pullx.xvg wron
>      (chris.neale at utoronto.ca)
>   4. Simulation of CNT with Amber forcefield (majid hasan)
>   5. Re: Simulation of CNT with Amber forcefield (Justin A. Lemkul)
>   6. protein-ligand complex tutorial (ahmet y?ld?r?m)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 18 Apr 2011 07:27:27 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] Re: energy group exclusions
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4DAC201F.2010901 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> Sikandar Mashayak wrote:
> > Also, what about non-bonded interactions within the protein? Does
> > exclusion group only exclude the non-bonded interactions between two
> > different molecules and non-bonded interactions within the single
> > molecule atoms are still computed?
> >
>
> Nonbonded interactions are excluded between each defined pair.  Therefore,
> with
>
> energygrp_excl = Protein Protein SOL SOL
>
> you are excluding all nonbonded interactions between protein atoms (Protein
> Protein pair) and between solvent atoms (SOL SOL pair).  Protein-solvent
> interactions are calculated.  The use of energygrp_excl (as documented)
> indicates that only nonbonded interactions are affected.  That is, bonded
> energies should still be calculated for all groups.
>
> -Justin
>
> > On Sun, Apr 17, 2011 at 10:38 PM, Sikandar Mashayak
> > <symashayak at gmail.com <mailto:symashayak at gmail.com>> wrote:
> >
> >     Hi
> >
> >     When we define energy group exclusions e.g. like in manual energygrp
> >     excl = Protein Protein SOL SOL
> >     and do md rerun, then only non-bonded interactions between Protein
> >     and SOL are computed. I am wondering what happens to bonded
> >     interactions within the protein, do they contribute to energies even
> >     though we have excluded protein-protein interactions?
> >
> >     thanks
> >     sikandar
> >
> >
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
>
> ------------------------------
>
> Message: 2
> Date: Mon, 18 Apr 2011 13:41:42 +0200
> From: Dommert Florian <dommert at icp.uni-stuttgart.de>
> Subject: Re: [gmx-users] diverging temperature with pressure coupling
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <1303126902.2464.107.camel at fermi>
> Content-Type: text/plain; charset="utf-8"
>
> On Mon, 2011-04-18 at 11:42 +0200, David van der Spoel wrote:
> > On 2011-04-18 11.22, Dommert Florian wrote:
> > > Hello,
> > >
> > > oh this nasty ILs ;) I am currently investigating a similar problem,
> > > that deals with PR-coupling and my impression is that Leap-Frog is the
> > > problem and not PR. Currently I am running simulations with md-vv and
> > > MTTK to verify my ideas. On the other hand I am using two tc_groups for
> > > my ILs due their difference in size. Unfortunately you have not written
> > > which IL you deal with, but thinking about long chain ILs like
> > > [BMIM][Cl], or [BMIM][PF6], the degrees of freedom for the different
> > > molecules differ strongly. Here the big question is why does the
> > > barostat influence the thermostat. It seems one has to be very very
> > > careful, when choosing the coupling parameter for PR. I did a bunch of
> > > simulations just varying the coupling parameter and obtained large
> > > differences in the dynamics of my system, while static properties like
> > > RDF, density of mass, and pressure look quite fine. For example if I
> > > calculate the conductivity including correlation effects the values
> > > differ from 2 S/m up to 12 S/m. But so far I also have no idea why ???
> > > I am really happy when I finally got my results with vv and if you are
> > > interested I can report back to the list or off-list, just let me know.
> > >
> > > On the other hand I do not know if the force field could be a problem.
> > > PR changes the box size according to a Lagrangian equation of motion in
> > > contrast to Berendsen, which just does size rescaling. I do not know
> how
> > > sensible this equations of motions are in respect to the motion of the
> > > atoms. Perhaps one can try to perform simulation with a higher accuracy
> > > for the electrostatic interactions. I realized that the standard PME
> > > settings are quite poor for ILs. Perhaps the Berendsen pressure
> coupling
> > > can deal with this, because it forces the box to scale. PR follows its
> > > equations of motions and PERHAPS introduces artefacts if the
> integration
> > > of atomic trajectories is too inaccurate.
> > >
> > > So my PME settings are like this:
> > >
> > > rcut=1.3 ( here the force field tells you the number )
> > > pme_order=6
> > > fourierspacing=0.05
> > > rtol=1e-8
> > >
> > > This are just approximate values, exact numbers can be calculated by
> > > g_pme_error for your system.
> > >
> > Florian, these PME values are scary! Are you running in double precision
> > too, otherwise I guess it will be difficult to get the errors as low as
> > you want them.
>
> Hello David,
>
> these settings yield an accuracy of 10^-4 kJ/(mol nm), which should be
> captured by a single precision calculation, if I take into account that
> I have forces around 100kJ/(mol nm). Am I wrong ?
>
> > As regards the Temperature diversion (no pun intended), this is a known
> > issue also with Berendsen T,P coupling. The reason for this is lack of
> > interaction between the different subsystems. It is interesting to hear
> > the PR makes it worse though, because of the better ensemble properties.
> >
> > If this also has an effect on dynamic properties all of us are in even
> > more trouble. I recently had problems reproducing dielectric constants.
> > I will now  redo my simulation with Berendsen P-coupling instead of PR,
> > even though grompp tells me not to!
> >
>
> So I assume the rerun with Berendsen will give you faster dynamics,
> which I had when using Berendsen. However as you mentioned you get into
> problems for creating a correct canonical ensemble.
>
> Cheers,
>
> Flo
>
>
> > > Cheers,
> > >
> > > Flo
> > >
> > >
> > > On Sun, 2011-04-17 at 03:10 -0400, Roland Schulz wrote:
> > >> Forwarding this email from my group colleague:
> > >>
> > >>
> > >> Dear Gromacs users,
> > >>
> > >>
> > >>
> > >> I am trying to simulate a cellulose fiber in an ionic liquid solution
> > >> in the NPT ensemble.  During the simulation, the entire system is
> > >> coupled to a thermostat.  Yet, I observe an inhomogeneous temperature
> > >> distribution throughout my system (hot-solvent/cold-solute) when I use
> > >> Parrinello-Rahman pressure coupling but NOT when I employ Berendsen
> > >> pressure coupling.  I have tested velocity-rescaling and the
> > >> Nose-Hoover scheme to keep the temperature constant and in both cases
> > >> Parrinello-Rahman pressure coupling seems to cause the solute’s
> > >> temperature to become significantly lower than the solvent’s (to
> > >> decompose temperatures, I am using “mdrun -rerun” with a run input
> > >> that defines tc_grps separately).
> > >>
> > >>
> > >>
> > >> I was wondering whether there were any known algorithmic reasons for
> > >> this unphysical temperature gradient when using Parrinello-Rahman
> > >> pressure coupling.
> > >>
> > >> Thank you.
> > >>
> > >> Barmak
> > >>
> > >>
> > >> Comment from me: The effect is large. The ionic liquid is 5 degrees
> > >> higher and the cellulose is 50 degrees lower (after 50ps, after that
> > >> it stays constant). With Berendsen pressure both parts fluctuate
> > >> around the same target temperature (as one would expect). Any reason
> > >> why one doesn't get the correct temperature with rerun? Or is their a
> > >> better way to get the temperature for different groups(for a
> > >> simulation with just one tc-group)? Any reason why Parrinello-Rahman
> > >> pressure coupling would have this effect on the temperature?
> > >>
> > >>
> > >> Roland
> > >>
> > >>
> > >> --
> > >> ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
> > >> 865-241-1537, ORNL PO BOX 2008 MS6309
> > >> --
> > >> gmx-users mailing list    gmx-users at gromacs.org
> > >> http://lists.gromacs.org/mailman/listinfo/gmx-users
> > >> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > >> Please don't post (un)subscribe requests to the list. Use the
> > >> www interface or send it to gmx-users-request at gromacs.org.
> > >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > >
> >
> >
> > --
> > David van der Spoel, Ph.D., Professor of Biology
> > Dept. of Cell & Molec. Biol., Uppsala University.
> > Box 596, 75124 Uppsala, Sweden. Phone:        +46184714205.
> > spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
>
>
> --
> Florian Dommert
> Dipl. - Phys.
>
> Institute for Computational Physics
> University Stuttgart
>
> Pfaffenwaldring 27
> 70569 Stuttgart
>
> EMail: dommert at icp.uni-stuttgart.de
> Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert
>
> Tel.: +49 - (0)711 - 68563613
> Fax.: +49 - (0)711 - 68563658
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> ------------------------------
>
> Message: 3
> Date: Mon, 18 Apr 2011 11:53:28 -0400
> From: chris.neale at utoronto.ca
> Subject: [gmx-users] Cylinder Pulling output file pullx.xvg wron
> To: gmx-users at gromacs.org
> Message-ID: <20110418115328.1gv8f4f0asg04gw8 at webmail.utoronto.ca>
> Content-Type: text/plain;       charset=ISO-8859-1;     DelSp="Yes";
>        format="flowed"
>
> That part of the pull code has a different printf statement in version
> 4.5.3. Can you test 4.0.7 output vs. 4.5.3 output and see if 4.5.3 is
> correct? You could simple use nsteps=0 genvel=no and load a .gro with
> no velocities in your mdrun.
>
> Chris.
>
> -- original message --
>
> I am trying cylinder pulling as an option of umbrella sampling using
> gromacs
> 4.0.7. Things seem to work but I noticed that in the output file pullx.xvg,
> the referece group's postion is always 0. I don't think it is right. When I
> use position pulling, the reference position is never 0.
>
> Thanks for you help.
> Kun
>
> Below is my .mdp file
> pull                    = umbrella
> pull_geometry           = cylinder
> pull_r1                 = 1.0
> Pull_r0                 = 1.0
> pull_dim                = N N Y
> pull_start              = yes
> pull_init1              = 0.0
> pull_ngroups            = 1
> pull_group0             = group0
> pull_group1             = group1
> pull_rate1              = 0.01
> pull_vec1               = 0.0 0.0 -1.0
> pull_k1                 = 3000      ; kJ mol^-1 nm^-2
> pull_nstxout            = 1000
> pull_nstfout            = 1000
>
> Here is the output:
>
> @    title "Pull COM"
> @    xaxis  label "Time (ps)"
> @    yaxis  label "Position (nm)"
> @TYPE xy
> @ view 0.15, 0.15, 0.75, 0.85
> @ legend on
> @ legend box on
> @ legend loctype view
> @ legend 0.78, 0.8
> @ legend length 2
> @ s0 legend "0 Z"
> @ s1 legend "1 dZ"
> 0.0000  0   5.69818
> 2.0000  0   5.67685
> 4.0000  0   5.68564
> 6.0000  0   5.65461
> 8.0000  0   5.63482
> 10.0000 0   5.61658
> 12.0000 0   5.61679
> 14.0000 0   5.54434
> 16.0000 0   5.55352
> 18.0000 0   5.4964
> -------------- next part -------------
>
>
>
> ------------------------------
>
> Message: 4
> Date: Mon, 18 Apr 2011 10:17:12 -0700 (PDT)
> From: majid hasan <pu_majidhasan at yahoo.com>
> Subject: [gmx-users] Simulation of CNT with Amber forcefield
> To: gms-users mailing list <gmx-users at gromacs.org>
> Message-ID: <674190.93212.qm at web38304.mail.mud.yahoo.com>
> Content-Type: text/plain; charset="us-ascii"
>
> Dear All,
>
> I am doing a DNA-CNT simulation, and I am trying to generate a topology of
> CNT
> using Amber99, which has been used for such systems, and CNT atoms are
> modeled
> using sp2 carbon parameters.
>
> But when I try to create topology file using: pdb2gmx -f cnt.pdb -p
> cnt.top, and
> Amber99 forcefield, I get this error:
> Fatal Error:
> Atom C in residue C 1 was not found in rtp entry RCN with 30 atoms while
> sorting
> atoms.
>
> During the execution, it says "There are 1 chains and 0 blocks of water and
> 1
> residues with 168 atoms" after analyzing pdb file.
>
> So I suspect problem is that it reads carbon as a residue in my .pdb file.
>
> If this is the problem, then how do I make sure that it reads carbon as an
> atom
> and not a residue?
>
> My .pdb file has entries of the form:
> ATOM  1   C     C  A   1  4.039    ....
> ATOM  2   C     C  A   1  3.97      ....
>
> Thanks for your help,
> Majid
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> ------------------------------
>
> Message: 5
> Date: Mon, 18 Apr 2011 13:25:39 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] Simulation of CNT with Amber forcefield
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4DAC7413.9090109 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> majid hasan wrote:
> > Dear All,
> >
> > I am doing a DNA-CNT simulation, and I am trying to generate a topology
> > of CNT using Amber99, which has been used for such systems, and CNT
> > atoms are modeled using sp2 carbon parameters.
> >
> > But when I try to create topology file using: pdb2gmx -f cnt.pdb -p
> > cnt.top, and Amber99 forcefield, I get this error:
>
> Have you created an .rtp entry for your CNT?  I doubt that it's even
> possible
> for cyclic molecules like this one.  pdb2gmx is only useful for linear
> molecules
> composed of repeating building blocks, with limited support for branching.
>  You
> may want to consult:
>
> http://www.gromacs.org/Documentation/How-tos/Carbon_Nanotube
>
> Some of that information is outdated, but there is a plethora of
> information in
> the list archive about proper CNT topology generation.  Search for posts by
> Christopher Stiles.
>
> > Fatal Error:
> > Atom C in residue C 1 was not found in rtp entry RCN with 30 atoms while
> > sorting atoms.
> >
>
> This answers my question above.  Your structure is being interpreted as
> RNA.
> Without significant effort and perhaps code modification, pdb2gmx is not
> likely
> to be useful here.
>
> > During the execution, it says "There are 1 chains and 0 blocks of water
> > and 1 residues with 168 atoms" after analyzing pdb file.
> >
> > So I suspect problem is that it reads carbon as a residue in my .pdb
> file.
> >
> > If this is the problem, then how do I make sure that it reads carbon as
> > an atom and not a residue?
> >
> > My .pdb file has entries of the form:
> > ATOM  1   C     C  A   1  4.039    ....
> > ATOM  2   C     C  A   1  3.97      ....
> >
>
> Well, you've named your residues "C" and the component atoms "C" so there's
> no
> real confusion about anything.  It's also not the source of your problems.
>
> g_x2top may be a useful program for generating a topology, or perhaps other
> software that is entirely unrelated to Gromacs.
>
> -Justin
>
> > Thanks for your help,
> > Majid
> >
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
>
> ------------------------------
>
> Message: 6
> Date: Mon, 18 Apr 2011 20:40:49 +0300
> From: ahmet y?ld?r?m <ahmedo047 at gmail.com>
> Subject: [gmx-users] protein-ligand complex tutorial
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <BANLkTi=QgPp3bc+egScOMvrUVR7Acfwo8g at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear Justin,
>
> You prepared a useful tutorial. if you used PO4 ligand (which has 2
> molecule) instead of 1JZ4 ligand from 3HTB.pdb, Then, in the .itp and .gro
> files of ligand because of 2 molecule, what change?
> Can you give some hint?
> Thanks
>
> 3HTB.pdb
> ....
>
> TER 1365 ASN A 163
> HETATM 1366 P PO4 A 165 15.430 -26.507 12.040 0.70 13.01 P
> HETATM 1367 O1 PO4 A 165 16.899 -26.359 11.761 0.70 8.42 O
> HETATM 1368 O2 PO4 A 165 14.565 -25.571 11.281 0.70 12.47 O
> HETATM 1369 O3 PO4 A 165 15.071 -28.010 11.811 0.70 11.58 O
> HETATM 1370 O4 PO4 A 165 15.042 -26.318 13.543 0.70 11.36 O
> HETATM 1371 P PO4 A 166 21.741 0.620 -18.648 0.50 20.49 P
> HETATM 1372 O1 PO4 A 166 23.073 -0.065 -18.917 0.50 18.04 O
> HETATM 1373 O2 PO4 A 166 21.958 2.010 -19.153 0.50 19.25 O
> HETATM 1374 O3 PO4 A 166 20.616 -0.014 -19.484 0.50 14.22 O
> HETATM 1375 O4 PO4 A 166 21.425 0.662 -17.127 0.50 15.77 O
> HETATM 1376 C4 JZ4 A 167 24.294 -24.124 -0.071 1.00 16.39 C
> ..
>
>
>
> --
> Ahmet YILDIRIM
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> End of gmx-users Digest, Vol 84, Issue 150
> ******************************************
>



-- 
Kun Huang
Department of Physics, Rensselaer Polytechnic Institute.
Troy, NY. 12180.
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