[gmx-users] a problem,Thank you
Maik Goette
mgoette at mpi-bpc.mpg.de
Mon Jan 21 09:44:36 CET 2008
This has been discussed several times...
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Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Germany
Tel. : ++49 551 201 2310
Fax : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
mgoette2[at]gwdg.de
WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/
jdy19862002 at 126.com wrote:
>
> I use ffamber94 in gromacs,and I also use spc water model
> However,I get wrong information when I am running grompp
>
> Fatal error:
> [ file "/usr/local/gromacs/share/gromacs/top/spc.itp", line 41 ]:
> Atom index (1) in settles out of bounds (1-0)
>
> I don't know how to solve it ,please help me
>
> Thank you!!!
>
>
>
>
>
>
> 在2008-01-20，gmx-users-request at gromacs.org 写道：
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> Today's Topics:
>
> 1. source code change (avinash kumar)
> 2. Re: source code change (David van der Spoel)
> 3. Re: GMX CPMD K+ ion problem (ggroenh)
> 4. Re: problem regarding grompp (kinshuk at chem.iitb.ac.in)
> 5. Re: problem regarding grompp (Mark Abraham)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sat, 19 Jan 2008 21:01:01 +0530
> From: "avinash kumar" <avinashk.iit.kgp at gmail.com>
> Subject: [gmx-users] source code change
> To: gmx-users at gromacs.org
> Message-ID:
> <7166960c0801190731p7c194427tb8fbcbad923ed7d7 at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hello all,
>
> Thank you Xavier for your reply. I will explain why I want to change
> the source code. I have to implement a modified Lennard Jones
> potential,
>
> ⎧
> ⎪
> ⎨ 4 *epsilon{( _σ_ )^12 − (_σ_ )^6} − VLJ (rc ), r ≤ rc ,
> r r
>
> V (r) =
> ⎪
> ⎩ 0, r > rc ,
>
> The original Lennard Jones potential has no -VLJ(rc) term. This means
> I want to subtract some constant from the Lennard Jones potential
> which the GROMACS will calculate. Please tell me where in the GROMACS
> source code should I make a change so that it will be implemented.
> Afterwards will I need to compile it again?
>
> Thanks in advance,
> Avinash
>
> ------------------------------
>
> Message: 2
> Date: Sat, 19 Jan 2008 16:34:18 +0100
> From: David van der Spoel <spoel at xray.bmc.uu.se>
> Subject: Re: [gmx-users] source code change
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4792187A.6060302 at xray.bmc.uu.se>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> avinash kumar wrote:
> > Hello all,
> >
> > Thank you Xavier for your reply. I will explain why I want to change
> > the source code. I have to implement a modified Lennard Jones
> > potential,
> >
> > ?
> > ?
> > ? 4 *epsilon{( _?_ )^12 - (_?_ )^6} - VLJ (rc ), r ? rc ,
> > r r
> >
> > V (r) =
> > ?
> > ? 0, r > rc ,
> >
> > The original Lennard Jones potential has no -VLJ(rc) term. This means
> > I want to subtract some constant from the Lennard Jones potential
> > which the GROMACS will calculate. Please tell me where in the GROMACS
> > source code should I make a change so that it will be implemented.
> > Afterwards will I need to compile it again?
> >
> Why not use one of the built-in shift potentials? This change will have
> no effect on the dynamics and only add a constant to the overall energy.
> Another alternative is to use a tabulated potential.
>
>
> > Thanks in advance,
> > Avinash
> >
> >
> > ------------------------------------------------------------------------
> >
> > _______________________________________________
> > gmx-users mailing list gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before posting!
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> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>
> --
> David van der Spoel, Ph.D.
> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
> spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
>
>
> ------------------------------
>
> Message: 3
> Date: Sat, 19 Jan 2008 19:49:58 +0100
> From: ggroenh <ggroenh at gwdg.de>
> Subject: [gmx-users] Re: GMX CPMD K+ ion problem
> To: gmx-users at gromacs.org
> Message-ID: <5914BAA8-8E0C-457B-AE18-800940935C01 at gwdg.de>
> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
>
> >
>
> Before step 1, gromacs outputs the number of atoms per QM layer, e.g.
>
> Reading file topol.tpr, VERSION 3.3_rc3 (single precision)
> QM/MM calculation requested.
> Layer 0
> nr of QM atoms 20
> QMlevel: CASSCF/3-21G,CASelectrons=6,CASorbitals=6
>
>
> How much are there in your simulaiton? This might tell if it goes
> wrong in gromacs side, or in cpmd.
>
> Gerrit
>
>
> > We pointed qm group in index .
> > ,,,,,,,,,,,,,,,,,,,,,,,,,,,
> > [ QM ]
> > 17 50 147 180 310 343 440 473 489
> > ...........................
> > and mdp,
> > ............
> > ; OPTIONS FOR QMMM calculations
> > QMMM = yes
> > ; Groups treated Quantum Mechanically
> > QMMM-grps = QM
> > ; QM method
> > QMmethod = CPMD
> > ; QMMM scheme
> > QMMMscheme = normal
> > ; QM basisset
> > QMbasis = STO-3G
> > ; QM charge
> > QMcharge = 1
> > .........
> >
> > CPMD_inp.tmpl:
> > .......
> > &ATOMS
> > *O_VDB_BLYP.psp FORMATTED
> > LMAX=P
> > *K_VDB_BLYP.psp FORMATTED
> > LMAX=P LOCAL=S
> > .......
> >
> > All these gives such CPMD_inp.run
> > .............
> > &ATOMS
> > *O_VDB_BLYP.psp FORMATTED
> > LMAX=P
> > 8
> > 14.8440376 8.2394453 13.9464178
> > 10.7622295 7.4646576 9.5055617
> > 7.7575652 10.3370411 13.7574452
> > 11.9716541 12.9448630 16.9321848
> > 12.6519555 17.0644656 12.7936849
> > 8.1544076 15.0802534 10.3559384
> > 12.5952637 12.5102260 6.8410481
> > 17.0739143 12.9448630 9.8079179
> > &END
> > ..............
> >
> > Potassium (9th atom) just skipped.
> > Any clue?
> >
> >
> >
> > On Jan 18, 2008 7:23 PM, Marius Retegan <marius.s.retegan at gmail.com>
> > wrote:
> >
> >> For the Gromacs-CPMD interface you have to specify the QM groups in
> >> your
> >> .mdp file like this "QMMM-grps = QM_part". Then open
> >> your
> >> index file and create an atom group with the same name "QM_part"
> >> and add in
> >> it all atoms that you want to treat with CPMD.
> >> If this doesn't work you should send to the list a output of you
> >> calculation.
> >> Marius Retegan
> >>
> >>
> >> On Jan 18, 2008 12:25 PM, Andrey V Golovin < golovin at belozersky.msu.ru
> >> >
> >> wrote:
> >>
> >>> Dear all,
> >>> We successfully passed all examples in GMX-CPMD and some other stuff
> >>> with amberff with common atoms, but since we trying to deal with K+
> >>> (potassium) in QM part, we see every time absence of potassium in
> >>> CPMD_inp.run, it's just skipped. In very beginning CPMD shows
> >>> right number
> >>> of atoms in QM group, but K is not mentioned in cpmd input file.
> >>>
> >>> Potassium and pseudopotential was included in CPMD_inp.tmpl.
> >>> We checked different ways of including Potassium in ff, like
> >>> amber_XX or
> >>> just K+.
> >>> Pseudopotential was build with Ultrasoft Pseudopotential Package.
> >>> Gmx-cpmd was compiled from site P. K. Biswas.
> >>>
> >>> Any ideas?
> >>> Thanks in advance, Andrey
> >>>
> >>> --
> >>> Best regards, Andrey
> >>> ------------------------------------------------------------------------------------------------
> >>>
> >>> Andrey V. Golovin
> >>> Ph.D, Assistant professor tel: +7 (495) 939-5305
> >>> Bioengineering and
> >>> Bioinformatics Department
> >>> Moscow State University fax: +7 (495) 939-3181
> >>> 119992 Moscow E-mail: golovin at genebee.msu.su
> >>> Russia web: http://rnp-group.genebee.msu.su
> >>> ------------------------------------------------------------------------------------------------
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>> _______________________________________________
> >>> gmx-users mailing list gmx-users at gromacs.org
> >>> http://www.gromacs.org/mailman/listinfo/gmx-users
> >>> Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
> >>>
> >>
> >>
> >> _______________________________________________
> >> gmx-users mailing list gmx-users at gromacs.org
> >> http://www.gromacs.org/mailman/listinfo/gmx-users
> >> Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
> >>
> >
> >
> >
> > --
> > Best regards, Andrey
> > ------------------------------------------------------------------------------------------------
> > Andrey V. Golovin
> > Ph.D, Assistant professor tel: +7 (495) 939-5305
> > Bioengineering and
> > Bioinformatics Department
> > Moscow State University fax: +7 (495) 939-3181
> > 119992 Moscow E-mail: golovin at genebee.msu.su
> > Russia web: http://rnp-group.genebee.msu.su
> > ------------------------------------------------------------------------------------------------
> > -------------- next part --------------
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> > URL: http://www.gromacs.org/pipermail/gmx-users/attachments/20080119/30cf38cd/attachment.html
> >
> > ------------------------------
> >
> > _______________________________________________
> > gmx-users mailing list
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> > http://www.gromacs.org/mailman/listinfo/gmx-users
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> > posting!
> >
> > End of gmx-users Digest, Vol 45, Issue 77
> > *****************************************
>
> --
> Gerrit Groenhof
> MPI biophysical chemistry
> Goettingen
> Germany
>
>
>
> ------------------------------
>
> Message: 4
> Date: Sun, 20 Jan 2008 09:27:54 +0530 (IST)
> From: kinshuk at chem.iitb.ac.in
> Subject: Re: [gmx-users] problem regarding grompp
> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> Message-ID: <49286.10.12.1.14.1200801474.squirrel at www.chem.iitb.ac.in>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Thanks for giving me insight to resolve the problem regarding grompp.
> Now i came across new problem regarding energy minimization
> MDRUN(mdrun)step while giving this command to command prompt.
> {mdrun -v -s em.tpr -o em.trr -e em.edr -c after_em.gro -g emlog.log }
> I came across this problem which i am mentioning below.
>
>
> Reading file em.tpr, VERSION 3.3.1 (single precision)
> Loaded with Money
>
>
> Back Off! I just backed up em.edr to ./#em.edr.2#
> Steepest Descents:
> Tolerance (Fmax) = 1.00000e+02
> Number of steps = 4000
> -------------------------------------------------------1.31850e+12, atom=
> 1924
> Program mdrun, VERSION 3.3.1
> Source code file: nsgrid.c, line: 226
>
> Range checking error:
> Explanation: During neighborsearching, we assign each particle to a grid
> based on its coordinates. If your system contains collisions or parameter
> errors that give particles very high velocities you might end up with some
> coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
> put these on a grid, so this is usually where we detect those errors.
> Make sure your system is properly energy-minimized and that the potential
> energy seems reasonable before trying again.
>
> Variable ci has value -2147483648. It should have been within [ 0 .. 216 ]
> Please report this to the mailing list (gmx-users at gromacs.org)
> -------------------------------------------------------
>
> What should be problem? I am attaching emergy minimization em.mdp file.
> For getting insight about i will be thankful to you.
> KINSHUK
>
>
>
>
> > kinshuk at chem.iitb.ac.in wrote:
> >> Hi all,
> >> I have been trying to simulate peptide (octa alanine). In genbox i have
> >> inserted 40 molecule of guanidium ion & 800 water molecule (by -ci &
> >> maxsol option in gromacs 3.3.3)then again with genbox i added 40
> >> molecules of thiocynate ion & 80 water molecules as above mentioned way.
> >> When i tried to do grompp for energy minimization i was encountered with
> >> many warning listed below though i have included the *.itp files of both
> >> ions in the topology *.top file of peptide.I need some insight about
> >> this
> >> so that i can resolve this problem.
> >>
> >> I have attached the em.mdp file along with this mail.
> >
> > This is not the problem, but your T-coupling groups aren't useful. See
> > http://wiki.gromacs.org/index.php/thermostats
> >
> >> If i will be getting help i'll be thankful for you.
> >
> > The order of molecules in your .top files [ molecules ] section probably
> > doesn't match the order of molecules in your structure file. See chapter
> > 5 of the GROMACS manual if you don't understand this.
> >
> > Mark
> > _______________________________________________
> > gmx-users mailing list gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
> >
> -------------- next part --------------
> ;
> ; Input file
> ;
> title = Octamer ; a string
> cpp = /lib/cpp ; c-preprocessor
> define = -DFLEX_SPC
> dt = 0.002 ; time step
> integrator = steep
> nsteps = 4000 ; number of steps
> nstcomm = 1 ; reset c.o.m. motion
> nstxout = 2000 ; write coords
> nstvout = 50 ; write velocities
> nstlog = 50 ; print to logfile
> nstenergy = 50 ; print energies
> energygrps = System
> nstlist = 10 ; update pairlist
> ns_type = grid
> constraint_algorithm = shake
> shake_tol = 0.0001
> coulombtype = PME
> vdwtype = shift
> rlist = 1.4 ; cut-off for ns
> rvdw = 1.4
> rvdw_switch = 0.8
> rcoulomb = 1.4
> rcoulomb_switch = 0.8
> tcoupl = berendsen ; temperature bath (yes,no)
> ref_t = 298
> tc_grps = Protein
> tau_t = 0.1
> Pcoupl = no
> tau_p = 0.5
> ref_p = 1.0
> gen_vel = yes ; generate initial velocities
> gen_temp = 298 ; initial temperature
> gen_seed = 173529 ; random seed
> emtol = 100
> emstep = 0.01
>
> ------------------------------
>
> Message: 5
> Date: Sun, 20 Jan 2008 16:02:45 +1100
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] problem regarding grompp
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4792D5F5.1080202 at anu.edu.au>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> kinshuk at chem.iitb.ac.in wrote:
> > Thanks for giving me insight to resolve the problem regarding grompp.
> > Now i came across new problem regarding energy minimization
>
> Please start a new email thread for a new problem. The subject line is
> your best chance to attract someone who can help you, so make it
> succint, relevant and informative.
>
> > MDRUN(mdrun)step while giving this command to command prompt.
> > {mdrun -v -s em.tpr -o em.trr -e em.edr -c after_em.gro -g emlog.log }
> > I came across this problem which i am mentioning below.
> >
> >
> > Reading file em.tpr, VERSION 3.3.1 (single precision)
> > Loaded with Money
> >
> >
> > Back Off! I just backed up em.edr to ./#em.edr.2#
> > Steepest Descents:
> > Tolerance (Fmax) = 1.00000e+02
> > Number of steps = 4000
> > -------------------------------------------------------1.31850e+12, atom=
> > 1924
> > Program mdrun, VERSION 3.3.1
> > Source code file: nsgrid.c, line: 226
> >
> > Range checking error:
> > Explanation: During neighborsearching, we assign each particle to a grid
> > based on its coordinates. If your system contains collisions or parameter
> > errors that give particles very high velocities you might end up with some
> > coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
> > put these on a grid, so this is usually where we detect those errors.
> > Make sure your system is properly energy-minimized and that the potential
> > energy seems reasonable before trying again.
> >
> > Variable ci has value -2147483648. It should have been within [ 0 .. 216 ]
> > Please report this to the mailing list (gmx-users at gromacs.org)
> > -------------------------------------------------------
> >
> > What should be problem? I am attaching emergy minimization em.mdp file.
>
> This is symptomatic of the kinds of problems discussed here...
> http://wiki.gromacs.org/index.php/blowing_up
>
> Because grompp returned you a .tpr file, your topology may have been
> well-formed. You should run grompp again and pay particular attention to
> any warnings it gives you. Even if it doesn't warn you about anything,
> the odds are excellent that despite being well-formed grammatically, the
> contents of your .top file lead to nonsense physics. Then large force on
> atoms can cause the above symptoms in EM.
>
> You should check your topology carefully, consulting with Chapter 5 of
> the manual where you need to. Break the structure & topology up into
> manageable chunks, and try an EM on an isolated molecule of each type to
> see which bit of the topology is broken.
>
> Mark
>
>
> ------------------------------
>
> _______________________________________________
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>
> End of gmx-users Digest, Vol 45, Issue 79
> *****************************************
>
>
>
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