[gmx-users] minimization

Thu Aug 13 17:29:57 CEST 2009

Dear MARK and Tsjerk

Thanks for your advises.....
Considering to my input and out put I should say that I mention to the
chain and in pdb file chain A and chain B are separate....
also I cheked toplogy and the structure after pdb2gmx...the atoms in
topology are reasonable and gro file does not have any problem...

and also I told you that the structure also have problem with amber
forcefield...it seems that  the structure has problem with All ATom
forcefield........

The energy of structure after minimization by gromacs is :

Step 1427, Epot=-4.410279e+04, Fnorm=2.888e+01, Fmax=8.733e+02 (atom 42)
Step 1428, Epot=-4.410310e+04, Fnorm=7.615e+00, Fmax=8.470e+01 (atom 2718)

writing lowest energy coordinates.

Polak-Ribiere Conjugate Gradients converged to Fmax < 100 in 1428 steps
Potential Energy  = -4.4103102e+04
Maximum force     =  8.4704674e+01 on atom 2718
Norm of force     =  7.6154613e+00

yours

morteza

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> Today's Topics:
>
>    1. minimization (Morteza Khabiri)
>    2. Re: minimization (Mark Abraham)
>    3. Re: Fatal Equilibration Errors (Bruce D. Ray)
>    4. Re: minimization (Tsjerk Wassenaar)
>    5. solvation (Jamie Seyed)
>    6. Re: solvation (Justin A. Lemkul)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 13 Aug 2009 11:30:03 +0200 (CEST)
> From: "Morteza Khabiri" <khabiri at greentech.cz>
> Subject: [gmx-users] minimization
> To: gmx-users at gromacs.org
> Message-ID:
> 	<25565.160.217.215.124.1250155803.squirrel at www.greentech.cz>
> Content-Type: text/plain;charset=iso-8859-2
>
> Dear Tsjerk
>
> Thanks for your suggestion...actually It is a crystal structure...the
> problem happen when I want to minimize the structure in vacuum....the box
> size is enough...but the problem is that the minimization is fine with
> gromacs forcefield but it is not ok with OPLSAA forcefiled....I tried to
> minimized structure well  by gromacs force file and the I took the
> minimized structure from gromacs forcefield and then I tried it in OPLSAA
> and the problem was the same as before... I also cut my structure to some
> pieces ( which I think that it is not reasonable) but I did it but still
> it is not working....and the interesting point is that the protein is
> working by gromacs forcefield well without any problem but when I want to
> use the OPLSAA force field the problem
> start and I could not minimized my system..I also try the AMBER forcefield
> but the AMBER also didi not work and the result was the same as OPLSAA,
> system was exploding.......when I want use all atom the problem appear and
> I really don't know how to manage it..I already tried different coulomb
> type algorythm and also different integrator,, different time
> step..different emtol........but none of them working.......
>
> I would be happy if somebody could suggest me how could I manage it with
> all atom forcefield...
>
> thanks
>
>
>
>
>
>
> ------------------------------
>
> Message: 2
> Date: Thu, 13 Aug 2009 20:56:22 +1000
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] minimization
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4A83F156.2020500 at anu.edu.au>
> Content-Type: text/plain; charset=ISO-8859-2; format=flowed
>
> Morteza Khabiri wrote:
>> Dear Tsjerk
>>
>> Thanks for your suggestion...actually It is a crystal structure...the
>> problem happen when I want to minimize the structure in vacuum....the
>> box
>> size is enough...but the problem is that the minimization is fine with
>> gromacs forcefield but it is not ok with OPLSAA forcefiled....
>
> That seems intrinsically improbable, unless the oplsaa .hdb and .tdb
> files are not coping with the structure (somehow) and generating a
> broken starting configuration and/or topology. What was the final PE and
> maximum force from the gromacs forcefield EM? I suggest you look
> carefully at the post-pdb2gmx oplsaa structure for steric clashes,
> unsatisified valences, etc., and then look at the progress of the
> corresponding minimization. You should see evidence of whatever is wrong.
>
> Mark
>
>> I tried to
>> minimized structure well  by gromacs force file and the I took the
>> minimized structure from gromacs forcefield and then I tried it in
>> OPLSAA
>> and the problem was the same as before... I also cut my structure to
>> some
>> pieces ( which I think that it is not reasonable) but I did it but still
>> it is not working....and the interesting point is that the protein is
>> working by gromacs forcefield well without any problem but when I want
>> to
>> use the OPLSAA force field the problem
>> start and I could not minimized my system..I also try the AMBER
>> forcefield
>> but the AMBER also didi not work and the result was the same as OPLSAA,
>> system was exploding.......when I want use all atom the problem appear
>> and
>> I really don't know how to manage it..I already tried different coulomb
>> type algorythm and also different integrator,, different time
>> step..different emtol........but none of them working.......
>>
>> I would be happy if somebody could suggest me how could I manage it with
>> all atom forcefield...
>>
>> thanks
>>
>>
>>
>>
>> _______________________________________________
>> gmx-users mailing list    gmx-users at gromacs.org
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>
>
> ------------------------------
>
> Message: 3
> Date: Thu, 13 Aug 2009 04:42:57 -0700 (PDT)
> From: "Bruce D. Ray" <brucedray at yahoo.com>
> Subject: Re: [gmx-users] Fatal Equilibration Errors
> To: gmx-users at gromacs.org
> Message-ID: <989464.1354.qm at web35801.mail.mud.yahoo.com>
> Content-Type: text/plain; charset="us-ascii"
>
> On Wednesday, August 12, 2009 at 8:47:33 PM, Nancy <nancy5villa at gmail.com>
> wrote:
>
>> In an earlier message, it was stated that topolbuild generated
> topologies with Gromos 53a6
>> and OPLS-AA force fields.  I am using
> topolbuild (version 1.2.2), and the only files in the
>> "dat/gromacs"
> directory are for the force fields: 43a1, 43a2, 43b1, 45a3, 53a5, and
> 53a6.
>> How is the OPLS-AA force field used?
>
> First, I need to thank you in particular.  First, while testing your
> molecules, I discovered a
> case in the as yet unreleased topolbuild 1.3 in which my dihedral
> selection method failed
> to select the dihedral choice with the maximum number of heavy atoms with
> OPLS-AA as
> the force field. Second, also because of this, I discovered what one
> downloads as a "Sybyl
> 2" structure from one source of small molecule structures and how to edit
> it so that it meets
> the syntax standards for a true mol2 file. Thank you very much for this
> assistance.
>
> In the earlier message, I stated that topolbuild 1.2.1 ( and 1.2.2)
> generates topologies for
> amber, gaff, glycam, 43a1, 43a2, 43b1, 45a3, 53a5, and
> 53a6.  I stated that the as yet
> unreleased topolbuild 1.3 will include OPLS-AA. The version of topolbuild
> you have,
> is 1.2.2. Would you like to beta test topolbuild 1.3?
>
>
> Sincerely,
>
>  --
> Bruce D. Ray, Ph.D.
> Associate Scientist
> IUPUI
> Physics Dept.
> 402 N. Blackford St.
> Indianapolis, IN  46202-3273
>
>
>
>
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> ------------------------------
>
> Message: 4
> Date: Thu, 13 Aug 2009 15:46:33 +0200
> From: Tsjerk Wassenaar <tsjerkw at gmail.com>
> Subject: Re: [gmx-users] minimization
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
> 	<8ff898150908130646j2e1f415ew41dc8c0092dc39d at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hmm, was the OPLSAA run following the GMX one on the dimer or also
> performed on the monomers? If you feed a multimeric protein without
> chain identifiers (like in a .gro file) to pdb2gmx, it will bind the
> different chains together. That would be a good cause for a crash. So
> I'd say check that first, and check the output from pdb2gmx
> thoroughly. Also see if you end up with each chain in its own .itp
> file.
>
> Cheers,
>
> Tsjerk
>
> 2009/8/13 Mark Abraham <Mark.Abraham at anu.edu.au>:
>> Morteza Khabiri wrote:
>>>
>>> Dear Tsjerk
>>>
>>> Thanks for your suggestion...actually It is a crystal structure...the
>>> problem happen when I want to minimize the structure in vacuum....the
>>> box
>>> size is enough...but the problem is that the minimization is fine with
>>> gromacs forcefield but it is not ok with OPLSAA forcefiled....
>>
>> That seems intrinsically improbable, unless the oplsaa .hdb and .tdb
>> files
>> are not coping with the structure (somehow) and generating a broken
>> starting
>> configuration and/or topology. What was the final PE and maximum force
>> from
>> the gromacs forcefield EM? I suggest you look carefully at the
>> post-pdb2gmx
>> oplsaa structure for steric clashes, unsatisified valences, etc., and
>> then
>> look at the progress of the corresponding minimization. You should see
>> evidence of whatever is wrong.
>>
>> Mark
>>
>>> I tried to
>>> minimized structure well  by gromacs force file and the I took the
>>> minimized structure from gromacs forcefield and then I tried it in
>>> OPLSAA
>>> and the problem was the same as before... I also cut my structure to
>>> some
>>> pieces ( which I think that it is not reasonable) but I did it but
>>> still
>>> it is not working....and the interesting point is that the protein is
>>> working by gromacs forcefield well without any problem but when I want
>>> to
>>> use the OPLSAA force field the problem
>>> start and I could not minimized my system..I also try the AMBER
>>> forcefield
>>> but the AMBER also didi not work and the result was the same as OPLSAA,
>>> system was exploding.......when I want use all atom the problem appear
>>> and
>>> I really don't know how to manage it..I already tried different coulomb
>>> type algorythm and also different integrator,, different time
>>> step..different emtol........but none of them working.......
>>>
>>> I would be happy if somebody could suggest me how could I manage it
>>> with
>>> all atom forcefield...
>>>
>>> thanks
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> 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/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
>>>
>> _______________________________________________
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>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> Junior UD (post-doc)
> Biomolecular NMR, Bijvoet Center
> Utrecht University
> Padualaan 8
> 3584 CH Utrecht
> The Netherlands
> P: +31-30-2539931
> F: +31-30-2537623
>
>
> ------------------------------
>
> Message: 5
> Date: Thu, 13 Aug 2009 11:37:00 -0400
> From: Jamie Seyed <jamie.seyed at gmail.com>
> Subject: [gmx-users] solvation
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
> 	<a9e5cd7b0908130837q38477e2djae8264d1ab896d72 at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear all,
> I want to know how can I use genbox to fill inside of the pore as well as
> a
> layer outside. From the "man genbox" page I try to use -shell with a
> negative value (?) but it put waters far from the outside of the pore and
> I
> think it does not care about the sign. It seems strange to me because when
> I
> had 10 10 10 in the last line of my f.gro, by a shell 0.5 or 0.2, I got a
> layer of few molecule around the pore, but when I change it to 1. 1. 1.,
> the
> water molecules generated far away. I appreciate if someone tell me (1)
> how
> I can add water inside the pore and (2) why changing the box size will
> give
> a opposite result. Please advise..Thanks in advance/Jamie
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> ------------------------------
>
> Message: 6
> Date: Thu, 13 Aug 2009 11:42:36 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] solvation
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4A84346C.405 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> Jamie Seyed wrote:
>> Dear all,
>> I want to know how can I use genbox to fill inside of the pore as well
>> as a layer outside. From the "man genbox" page I try to use -shell with
>> a negative value (?) but it put waters far from the outside of the pore
>> and I think it does not care about the sign. It seems strange to me
>> because when I had 10 10 10 in the last line of my f.gro, by a shell 0.5
>> or 0.2, I got a layer of few molecule around the pore, but when I change
>> it to 1. 1. 1., the water molecules generated far away. I appreciate if
>> someone tell me (1) how I can add water inside the pore and (2) why
>
> (1) The -vdwd option may help, or even -ci -nmol.  If you have a pore,
> wouldn't
> water diffuse in over time anyway during equilibration (assuming an
> otherwise
> correct setup and realistic physical model)?
>
> (2) If you haven't re-positioned your system within the box, it probably
> doesn't
> make any sense.  The Gromacs convention is to place the corner of the box
> at the
> coordinate origin, and everything else is relative to that.  Is a 1-nm
> cubic box
> large enough to encompass your system?  If not, genbox is doing what it's
> told -
> filling a 1-nm box near the origin, and leaving everything else out.
>
> -Justin
>
>> changing the box size will give a opposite result. Please advise..Thanks
>> in advance/Jamie
>>
>>
>> ------------------------------------------------------------------------
>>
>> _______________________________________________
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>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
>
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>
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