[gmx-users] a problem,Thank you
jdy19862002 at 126.com
jdy19862002 at 126.com
Mon Jan 21 03:47:01 CET 2008
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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--
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
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>>> 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
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>>
>
>
>
> --
> 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
> ------------------------------------------------------------------------------------------------
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>
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> *****************************************
--
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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