Re: [gmx-users] defining 2 posres at a time in mdp
define them in the same line. define = -DPOSRES_WATER -DPOSRES > hi all, > I want to define position restraints for a part of protein and water > molecules > also. I need to deinfe -DPOSRES and -DPOSRES_WATER at the same time. When > I do it on separate lines in the mdp file, only first line is being read > and accepted. Is there any way to include both of them in the same mdp > file simultaneously. > regards > anwar > - > > ___ > gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Dilraj Lama, Graduate student, Bioinformatics and Biomolecular Simualtion lab, Dept. of BSBE;IITK-kanpur, Uttar pradesh,India-208016. email:[EMAIL PROTECTED],[EMAIL PROTECTED] mob:09415473973 ___ gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] defining 2 posres at a time in mdp
hi all, I want to define position restraints for a part of protein and water molecules also. I need to deinfe -DPOSRES and -DPOSRES_WATER at the same time. When I do it on separate lines in the mdp file, only first line is being read and accepted. Is there any way to include both of them in the same mdp file simultaneously. regards anwar - ___ gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Lipid Bilayer Simulations
Hi, I am new to Gromacs, and I am working with lipid bilayer simulations. I am attempting to just run an energy minimization on a lipid bilayer so I can get a better feel for the program. I have taken the files dppc128.pdb, dppc.itp, lipid.itp and example2.itp from Peter Tieleman's website. Because I could not use teh pdb2gmx command, I started with the editconf command and then the genbox command, both of which seemed to run successfully. Then, I tried to do the preprocessing with the grompp command, but I received the error; Fatal Error: Found a second defaults directive, file "lipid.itp". When I removed lipid.itp from the topology file, I received the error; Fatal Error: Atomtype 'LC3' not found! As I said before, I am new to Gromacs, and I am not sure how to get around this problem. Do I need to put the dppc.itp and lipid.itp file together into one? Any help would be appreciated. Thanks, Mike Tomasini ___ gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] QMMM interface
It does not exist, but since gmx is open source, I suggest you give it a try. I suppose the input/output is similar to gamess-uk? In that case, have a look at mdlib/qmmm.c and gamess.c. Contact me off list at ggroenh<>gwdg.de if you need more help. Gerrit On Sep 28, 2006, at 3:01 PM, [EMAIL PROTECTED] wrote: 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 ___ gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Note, from 2005 on my email adress has changed to [EMAIL PROTECTED] ___ gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] cardiolipin / Cytochrome C
Viswanadham Sridhara wrote: Hello gmx users, Were there any previous molecular dynamics simulations done on cardiolipin / Cytochrome C binding? Dunno. There's no substitute for searching the literature. Any "pdb" files available for either Cardiolipin or cytochrome C,. any literature available / any tutorials. Dunno. Looking in the Protein Databank would be more profitable for you. http://www.rcsb.org/pdb/ Mark ___ gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] defining new residues?
[EMAIL PROTECTED] 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 This would be possible, however it would be unwise to extrapolate that a force field for peptide simulations is suitable for lipid-polymer simulations without serious evidence, such as previous studies, or the force field having been developed with this use in mind. Look in the polymer literature and see what force fields are used there. Simplest will be to use the software and the force fields described there, rather than choose GROMACS and have to work something in to fit. There are polymer force fields that work with GROMACS, I just don't know what they are... 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? Yep. Chapters 4 and 5 of the manual. They're pretty good, but not perfect. I'd recommend playing around doing some simulations to see how the pieces fit together before tinkering seriously with force fields. Mark ___ gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: gmx-users Digest, Vol 29, Issue 86
Yes that is fine. I don't want to go later than 5 though. Jason On 28-Sep-06, at 3:02 PM, [EMAIL PROTECTED] wrote: Send gmx-users mailing list submissions to gmx-users@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 [EMAIL PROTECTED] You can reach the person managing the list at [EMAIL PROTECTED] 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 ([EMAIL PROTECTED]) 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? ([EMAIL PROTECTED]) 8. Re: defining new residues? (Dongsheng Zhang) -- Message: 1 Date: Thu, 28 Sep 2006 20:38:56 +0800 (CST) From: "zzhwise1" <[EMAIL PROTECTED]> Subject: [gmx-users] energy minimization end too early! To: "gmx-users" Message-ID: <[EMAIL PROTECTED]> 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: [EMAIL PROTECTED] Subject: [gmx-users] QMMM interface To: gmx-users@gromacs.org Message-ID: <[EMAIL PROTECTED]> 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" <[EMAIL PROTECTED]> Subject: Re: [gmx-users] energy minimization end too early! To: "Discussion list for GROMACS users" Message-ID: <[EMAIL PROTECTED]> 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 <[EMAIL PROTECTED]> 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 listgmx-users@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 [EMAIL PROTECTED] 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" <[EMAIL PROTECTED]> Subject: Re: [gmx-users] Re: water molecules in vacuum simulation To: "Discussion list for GROMACS users" Message-ID:
Re: [gmx-users] defining new residues?
Hi Scott You can use PRODRG (available online) for generating topologies. Then you dont have to worry about playing with pdb2gmx. Cheers, - Rahul On Thu, 28 Sep 2006 [EMAIL PROTECTED] 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 listgmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] defining new residues?
Dongsheng Zhang wrote: 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, [EMAIL PROTECTED] 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 listgmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php an alternative that's in the works is the x2top program, which is simpler, since it is atom based, but you need just one configuration file. if you want to see a sample send me a coordinate file off-list. you will need at least the 3.3.1 CVS version for this though. -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] defining new residues?
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, [EMAIL PROTECTED] 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 listgmx-users@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 [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] defining new residues?
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 listgmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] cardiolipin / Cytochrome C
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. ___ gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Job Vacancy -MolNaC University of Salerno
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. ___ gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: water molecules in vacuum simulation
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, [EMAIL PROTECTED] <[EMAIL PROTECTED]> 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 fcxfcyfcz 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 [EMAIL PROTECTED] --- - ___ gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] energy minimization end too early!
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 <[EMAIL PROTECTED]> 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 ! 体 验 超 净 畅 享 健 康 结 婚 生 育 潮 接 踵 至 小 天 鹅 水 魔 方 喜 迎 黄 金 周 ___ gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] 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 ___ gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] QMMM interface
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 ___ gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] energy minimization end too early!
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 ! 体 验 超 净 畅 享 健 康 结 婚 生 育 潮 接 踵 至 小 天 鹅 水 魔 方 喜 迎 黄 金 周 ___ gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: water molecules in vacuum simulation
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 fcxfcyfcz 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 [EMAIL PROTECTED] --- - ___ gmx-users mailing listgmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
