[gmx-users] Re: gmx-users Digest, Vol 29, Issue 86
Jason O'Young
joyoung at uwo.ca
Thu Sep 28 21:40:39 CEST 2006
Yes that is fine. I don't want to go later than 5 though.
Jason
On 28-Sep-06, at 3:02 PM, gmx-users-request at gromacs.org wrote:
> Send gmx-users mailing list submissions to
> gmx-users at gromacs.org
>
> To subscribe or unsubscribe via the World Wide Web, visit
> http://www.gromacs.org/mailman/listinfo/gmx-users
> or, via email, send a message with subject or body 'help' to
> gmx-users-request at gromacs.org
>
> You can reach the person managing the list at
> gmx-users-owner at gromacs.org
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of gmx-users digest..."
>
>
> Today's Topics:
>
> 1. energy minimization end too early! (zzhwise1)
> 2. QMMM interface (pedros at ufp.pt)
> 3. Re: energy minimization end too early! (Tsjerk Wassenaar)
> 4. Re: Re: water molecules in vacuum simulation (David Mobley)
> 5. Job Vacancy -MolNaC University of Salerno (andrea correa)
> 6. cardiolipin / Cytochrome C (Viswanadham Sridhara)
> 7. defining new residues? (scott.t.milner at exxonmobil.com)
> 8. Re: defining new residues? (Dongsheng Zhang)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 28 Sep 2006 20:38:56 +0800 (CST)
> From: "zzhwise1" <zzhwise1 at 163.com>
> Subject: [gmx-users] energy minimization end too early!
> To: "gmx-users" <gmx-users at gromacs.org>
> Message-ID: <451BC260.00008B.27975 at bj163app88.163.com>
> Content-Type: text/plain; charset="gb2312"
>
> hi everyone
> today ,I do minimization with my system,my system with two face
> to face monolayers composed of ch3(ch2)13cooh,
> when i set the molecular as CHO group,it pass smoothly,because i
> want to pull the upper layer ,so i set the upper layer group DHO
> that has the same parameters with CHO itp , but the mdrun only
> reached 22th step and finished normally,which is too few to 5000
> steps!
> i want why !
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: http://www.gromacs.org/pipermail/gmx-users/attachments/
> 20060928/0127a11b/attachment-0001.html
>
> ------------------------------
>
> Message: 2
> Date: Thu, 28 Sep 2006 14:01:31 +0100
> From: pedros at ufp.pt
> Subject: [gmx-users] QMMM interface
> To: gmx-users at gromacs.org
> Message-ID: <20060928140131.i1nk3bcu6g408c4c at webmail.ufp.pt>
> Content-Type: text/plain; charset=ISO-8859-1; format="flowed"
>
>
> Dear Gromacs users,
>
> I have been using Pcgamess for QM calculations, which is a very fast
> (and free) program, and has some QMMM capabilities(but a size limit of
> about 1000 atoms ). I just found out that Gromacs now has QMMM
> capabilities with CPMD, Gaussian and Gamess(UK). Does any one know
> whether a Gromacs-PcGamess QMMM interface is planned? It would be
> great
> for those of us with small research budgets, and who cannot afford the
> comercial QM codes.
>
> Pedro
>
> ----------------------------------------------------------------
> Enviado por https://webmail.ufp.pt
>
>
>
>
> ------------------------------
>
> Message: 3
> Date: Thu, 28 Sep 2006 15:08:47 +0200
> From: "Tsjerk Wassenaar" <tsjerkw at gmail.com>
> Subject: Re: [gmx-users] energy minimization end too early!
> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> Message-ID:
> <8ff898150609280608w4305a048vdcc5f89ca84266c at mail.gmail.com>
> Content-Type: text/plain; charset=GB2312; format=flowed
>
> Hi Zzhwise1,
>
> Energy minimization does not need to run all steps. You define a
> maximum number, but maybe the minimum is already reached before that.
> On the other hand, the energy may have gone to infinity, which usually
> puts an end to minimization. Check the energies you get during/after
> minimization. Check for overlaps, bad starting structures, bad box,
> etc.
>
> Tsjerk
>
> On 9/28/06, zzhwise1 <zzhwise1 at 163.com> wrote:
>> hi everyone
>> today ,I do minimization with my system,my system with two
>> face to face
>> monolayers composed of ch3(ch2)13cooh,
>> when i set the molecular as CHO group,it pass smoothly,because i
>> want to
>> pull the upper layer ,so i set the upper layer group DHO that has
>> the same
>> parameters with CHO itp , but the mdrun only reached 22th step and
>> finished
>> normally,which is too few to 5000 steps!
>> i want why !
>>
>>
>>
>>
>>
>>
>> Ìå Ñé ³¬ ¾»¡¡³© Ïí ½¡ ¿µ
>> ½á »é Éú Óý ³± ½Ó õà ÖÁ¡¡Ð¡ Ìì ¶ì Ë® ħ ·½ ϲ Ó »Æ ½ð ÖÜ
>> _______________________________________________
>> gmx-users mailing list gmx-users at gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> 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
>>
>>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
> Dept. of Biophysical Chemistry
> University of Groningen
> Nijenborgh 4
> 9747AG Groningen, The Netherlands
> +31 50 363 4336
>
> ------------------------------
>
> Message: 4
> Date: Thu, 28 Sep 2006 08:42:46 -0700
> From: "David Mobley" <dmobley at gmail.com>
> Subject: Re: [gmx-users] Re: water molecules in vacuum simulation
> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> Message-ID:
> <bc2c99750609280842k23127638g41b3047860241bfa at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> This may be naive, but have you defined POSRES_WATER, i.e. in your top
> or mdp file? If not, the position restraints will be unused.
>
>
>
> On 9/28/06, anwar at cdfd.org.in <anwar at cdfd.org.in> wrote:
>> Hi all,
>> I am facing a problem in constraining the crystallographic water
>> molecules
>> during invacuo simulation. Even after including the oxygen atom
>> numbers
>> in the .top file for position restrain (given below), the dynamics
>> is going
>> the same way as it was without positoion restrain. Please Help me
>> out of
>> this.
>> #ifdef POSRES_WATER
>> ; Position restraint for each water oxygen
>> [ position_restraints ]
>> ; i funct fcx fcy fcz
>> 12448 1 1000 1000 1000
>> 12451 1 1000 1000 1000
>> 12454 1 1000 1000 1000
>> 12457 1 1000 1000 1000
>> 12460 1 1000 1000 1000
>> 12463 1 1000 1000 1000
>> 12466 1 1000 1000 1000
>> 12469 1 1000 1000 1000
>> 12472 1 1000 1000 1000
>> 12475 1 1000 1000 1000
>> 12478 1 1000 1000 1000
>> 12481 1 1000 1000 1000
>> 12484 1 1000 1000 1000
>> 12487 1 1000 1000 1000
>> 12490 1 1000 1000 1000
>> 12493 1 1000 1000 1000
>> 12496 1 1000 1000 1000
>> 12499 1 1000 1000 1000
>> 12502 1 1000 1000 1000
>> 12405 1 1000 1000 1000
>> #endif
>>
>> regards
>> Anwar
>> ----------------------
>> Mohd Anwaruddin
>> Project Assistant
>> C/o DR.H.A.Nagarajaram
>> Lab of Computational Biology and Bioinformatics
>> Center for DNA Fingerprinting and Diagnostics(CDFD)
>> Nacharam
>> Hyderabad-500 076
>> INDIA.
>> Tel: +91-8413-235467,68,69,70 ext 2019
>> anwar.m1 at gmail.com
>> -----------------------
>>
>>
>>
>> -
>>
>> _______________________________________________
>> gmx-users mailing list gmx-users at gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> 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
>>
>
>
> ------------------------------
>
> Message: 5
> Date: Thu, 28 Sep 2006 18:05:53 +0200
> From: andrea correa <acorrea at unisa.it>
> Subject: [gmx-users] Job Vacancy -MolNaC University of Salerno
> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> Cc: lcavallo at unisa.it
> Message-ID: <200609281805.53193.acorrea at unisa.it>
> Content-Type: text/plain; charset="us-ascii"
>
>
> Applications are invited for a postdoctoral position in computational
> chemistry in the group of Luigi Cavallo in the Department of Chemistry
> at the University of Salerno, Italy. The initial appointment is for
> one year, with the possibility to renew for a second year on the
> condition that research funds are available.
>
>
> Candidates should have a Ph.D. in Chemistry, Physics, or related
> fields. A strong background in computational chemistry and programming
> skills are essential. The main theme of our research is to develop and
> apply state-of-the-art computational tools (electronic structure
> calculations, mainly) to achieve an understanding of reaction
> mechanisms and of intermolecular interactions. The systems of primary
> interest are organometallic complexes for homogeneous catalysis. For
> more information see http://www.chem.unisa.it/groups/molnac/.
>
> Interested candidates should send a letter of intent and a C.V. (by
> e-mail to lcavallo-at-unisa.it), and arrange for two letters of
> recommendation.
>
>
>
> ------------------------------
>
> Message: 6
> Date: Thu, 28 Sep 2006 13:48:50 -0400
> From: "Viswanadham Sridhara" <muta.mestri at gmail.com>
> Subject: [gmx-users] cardiolipin / Cytochrome C
> To: "GROMACS list" <gmx-users at gromacs.org>
> Message-ID:
> <a5e4ea9a0609281048x2042c264qcb7541c67bb746c9 at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hello gmx users,
>
> Were there any previous molecular dynamics simulations done on
> cardiolipin /
> Cytochrome C binding?
> Any "pdb" files available for either Cardiolipin or cytochrome C,. any
> literature available / any tutorials.
>
> Thanks in advance,
> -Vissu.
>
> --
> Viswanadham Sridhara,
> Research Assistant,
> Old Dominion University,
> Norfolk, Va-23529.
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: http://www.gromacs.org/pipermail/gmx-users/attachments/
> 20060928/eaeced0d/attachment-0001.html
>
> ------------------------------
>
> Message: 7
> Date: Thu, 28 Sep 2006 13:38:56 -0400
> From: scott.t.milner at exxonmobil.com
> Subject: [gmx-users] defining new residues?
> To: gmx-users at gromacs.org
> Message-ID:
> <OFB0CC1D96.7D5DCD45-
> ON852571F7.005F04FE-852571F7.0060F2E0 at exxonmobil.com>
>
> Content-Type: text/plain; charset=US-ASCII
>
> Hello -- I am interested in using gromacs to simulate polymers.
> Apparently
> the .rtp files within gromacs are defined for protein residues, not
> typical
> monomers being used in polymers. I don't know anything about
> proteins, but
> I would think that there is a strong analogy between proteins and
> polymers,
> in that linear polymers are composed of a succession of monomers
> (often,
> just the same monomer repeated), joined by single covalent bonds.
> Typical
> monomers I would be interested in are methylene (-CH2-), propylene
> (-CH(CH3)CH2-), styrene (-CH(C6H5)CH2-), and so forth. It would be
> very
> convenient if I could add these structures as new "residues" to the
> definitions of some of the force fields (e.g., OPLSAA and GMX), so
> that I
> could use pdb2gmx to generate topology files for a simulation, without
> having to generate the topology files by hand. Is there some
> documentation
> that describes the structure of the various files associated with a
> force
> field, and what information would then be required for defining new
> residues?
>
> Thanks for any help you can provide --
>
> Scott Milner
> ExxonMobil Research and Engineering
> 1545 Route 22 East
> Annandale, NJ 08801
> (908) 730-2309 phone
> (262) 313-2583 fax
>
>
>
> ------------------------------
>
> Message: 8
> Date: Thu, 28 Sep 2006 15:02:05 -0400
> From: Dongsheng Zhang <dong at pampas.chem.purdue.edu>
> Subject: Re: [gmx-users] defining new residues?
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <1159470125.12441.20.camel at pampas.chem.purdue.edu>
> Content-Type: text/plain
>
> It is possible to generate new "residues". First of all, you need to
> make a decision which force field you will use for your new residues.
> For example, you will choose opls. then you add one building block
> into
> ffoplsaa.rtp. As you read ffoplsaa.rtp, you can see that you need to
> specify atoms' name, type, and the partial charge, you also need to
> define bonds and the dihedral angle between atoms. When you build it,
> you need to refer ffoplsaanb.itp ffoplsaabon.itp and ffoplsaa.atp. You
> might modify aminoacids.dat, ffoplsaa-n.tdb' ffoplsaa-c.tdb as well.
>
>
> You can read the manual to get more information.
>
>
> On Thu, 2006-09-28 at 13:38 -0400, scott.t.milner at exxonmobil.com
> wrote:
>> Hello -- I am interested in using gromacs to simulate polymers.
>> Apparently
>> the .rtp files within gromacs are defined for protein residues,
>> not typical
>> monomers being used in polymers. I don't know anything about
>> proteins, but
>> I would think that there is a strong analogy between proteins and
>> polymers,
>> in that linear polymers are composed of a succession of monomers
>> (often,
>> just the same monomer repeated), joined by single covalent bonds.
>> Typical
>> monomers I would be interested in are methylene (-CH2-), propylene
>> (-CH(CH3)CH2-), styrene (-CH(C6H5)CH2-), and so forth. It would
>> be very
>> convenient if I could add these structures as new "residues" to the
>> definitions of some of the force fields (e.g., OPLSAA and GMX), so
>> that I
>> could use pdb2gmx to generate topology files for a simulation,
>> without
>> having to generate the topology files by hand. Is there some
>> documentation
>> that describes the structure of the various files associated with
>> a force
>> field, and what information would then be required for defining new
>> residues?
>>
>> Thanks for any help you can provide --
>>
>> Scott Milner
>> ExxonMobil Research and Engineering
>> 1545 Route 22 East
>> Annandale, NJ 08801
>> (908) 730-2309 phone
>> (262) 313-2583 fax
>>
>> _______________________________________________
>> gmx-users mailing list gmx-users at gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> 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
>
>
> End of gmx-users Digest, Vol 29, Issue 86
> *****************************************
More information about the gromacs.org_gmx-users
mailing list