Re: [gmx-users] Choosing water molecules and box type and dimensions
Justin, as always is absolutely right. The paper that I have suggested is just compare the different water models with the bulk properties. And the bio molecular forcefields are compatible with particular type water model. Like charmm force field is compatible with TIP3P water. On Fri, Apr 29, 2016 at 6:53 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 4/29/16 9:51 AM, zeineb SI CHAIB wrote: > >> Dear all, >> >> Thank your for your answers. >> >> @ Justin, >> >> Where can I found informations related to the compatibility of one water >> type with the force field that I choose for my protein? in other words >> "where can I found information about the water type that had been used for >> the parametrisation of my Force field"? >> >> > Read the primary literature for the force field you're using. That's of > course the first step, otherwise you wouldn't have chosen a force field > yet, right? :) > > Then look for subsequent citations of that force field in application > studies related to water. There are a few for each force field, but > generally the water model is considered part of the force field and it is > rare to deviate from this model. Don't do it unless you have a really, > really good reason. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > == > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Abhijit kayal Research Scholar Theoretical Chemistry IIT Kanpur -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Choosing water molecules and box type and dimensions
you can look the following paper for the properties of different water models. Simulating water with rigid non-polarizable models: a general perspective Phys. Chem. Chem. Phys., 2011, 13, 19663–19688. In this paper they compare all the water models based on their different thermodynamics and dynamical properties. It tuns out TIP4P/2005 water model is the best one which can mimic the bulk water most closely. On Fri, Apr 29, 2016 at 5:21 AM, zeineb SI CHAIB <zeineb...@hotmail.com> wrote: > Hi, > > I'm working on a protein and two cofactors and one substrate, I have too > simulate all this system on GROMACS. I'm in the first stage: choosing a > force field, box type and dimensions, water molecules...etc. > > I would like to know more about the water molecule types (I looked on the > internet but I didn't find much informations) (what is the difference > between them, according to what I should choose a type..etc) and the box > type and dimensions that I should choose? > > Thank you in advance for your help. > > Cordially. > > Zeineb. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Abhijit kayal Research Scholar Theoretical Chemistry IIT Kanpur -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] on the xmgrac for gromacs
the command is xmgrace, try with xmgrace -nxy. On Sun, Apr 26, 2015 at 7:01 AM, Brett brettliu...@163.com wrote: Dear All, For the grpmacs analysis purpose, from the official GRACE site I have downloaded and installed different versions of GRACE, some was said to definitely contains xmgrace. But after installation, none contains xmgrace, they contain grace or gr in the bin folder. After I invoke the grace or gr, both needs me input commands, and if I input grace -nxy potential.xvg, they did not work. My workstation is a red hat linux system, and I do not know whether there is X windows installed. Will you please let me know how to have my xmgrace -nxy potential.xvg function works? Brett -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Abhijit kayal Research Scholar Theoretical Chemistry IIT Kanpur -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] help on Graphene Nano Sheets
Hi Mercelo Copy the oplsaa.ff directory to your working directory. Then in ffnonbonded.itp file add the following lines.. opls_995 C 612.01100 0.000 A3.4e-01 3.61200e-01 opls_996 C 612.01100 0.000 A3.4e-01 3.61200e-01 opls_997 C 612.01100 0.000 A3.4e-01 3.61200e-01 Then in atomname2type.n2t file add the following lines. Copls_9950 12.011 2C 0.142 C 0.142 Copls_9960 12.011 3C 0.142 C 0.142 C 0.142 Copls_9970 12.011 1C 0.142 Then use g_x2top. This will work. On Thu, Apr 23, 2015 at 10:54 PM, Alex nedoma...@gmail.com wrote: I think we've covered this when I was having the same issue. If you're trying to simulate a multi-molecule system, then just copy the entire forcefield .ff folder to your local directory and modify the following files: ffbonded.itp ffnonbonded.itp atomnames2types.n2t No need to create rtp entries for graphene/nanotubes, so you can ignore that part of Andrea's tutorial. Instead of just C in his tutorial, come up with a unique label to avoid conflicts, which should then also be used in your PDB. Then what I would do is create a topology entry for just graphene and convert it to a stand-alone itp by stripping off system definitions. This is basically opening the top file, removing those definitions and resaving as *.itp. After that, you can just use pdb2gmx on the remaining parts of the system and complete the system topology by hand. I know, this sounds like a lot of manual tweaking, but this is the paradigm. Good luck! Alex MC I run a graphene nanolayer, usin the below description (from previous mail. MC Now i got an other error. It look like there is a conflict in a force MC field system, someone can suggest me how to modify it? MC the force field file came from Minoia advices, reported in the web side! MC / MC //Program grompp, VERSION 4.6.7// MC //Source code file: MC /home/marcello/DATI/software/gromacs-4.6.7/src/kernel/topio.c, line: 752// MC // MC //Fatal error:// MC //Syntax error - File forcefield.itp, line 31// MC //Last line read:// MC //'1 3 yes 0.5 0.5'// MC //Found a second defaults directive./* MC * -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Abhijit kayal Research Scholar Theoretical Chemistry IIT Kanpur -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] error in grompp if used TIP4p-Ew water at pdb2gmx
Yaap.. that was the mistak you were doing. On Thu, Apr 16, 2015 at 4:50 PM, Raj D gromacs.fo...@gmail.com wrote: Dear Abhijit, Thank you infact I myself figured out that now; while solvating I used spc216.gro instead of tip4 water model and the error now gone. Sorry for the trouble. Regards, Raja On Apr 16, 2015 4:10 PM, abhijit Kayal abhijitchemi...@gmail.com wrote: How did you solvate your system? What exact command did you use? On Thu, Apr 16, 2015 at 2:37 PM, Raj D gromacs.fo...@gmail.com wrote: Dear Users, I want to use TIP4P-Ew water model for my simulation of protein. Every time I select water model TIP4P-Ew option number 3 in pdb2gmx step it writes the toplogy and coordinate files and I use gmx ediconf and gmx solvate tool to prepare solvation system for simulation and at the stage of issuing grompp command for EM , it reports a typical coordinate file mismatch error between solvated.gro and topol.top . surprisingly if I selected any other water model other than TIP4P-Ew at the stage of pdb2gmx, the grompp steps went on right. Since there is no special mentioning in the pdb2gmx -h report or in manual about any special user interference needed to be there in using TIP4P-Ew in pdb2gmx , I wonder why it is behaving like this , I am using the latest version of gromacs-5.0.4. ? Kindly do the needful. With kind regards, Raja -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Abhijit kayal Research Scholar Theoretical Chemistry IIT Kanpur -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Abhijit kayal Research Scholar Theoretical Chemistry IIT Kanpur -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] error in grompp if used TIP4p-Ew water at pdb2gmx
How did you solvate your system? What exact command did you use? On Thu, Apr 16, 2015 at 2:37 PM, Raj D gromacs.fo...@gmail.com wrote: Dear Users, I want to use TIP4P-Ew water model for my simulation of protein. Every time I select water model TIP4P-Ew option number 3 in pdb2gmx step it writes the toplogy and coordinate files and I use gmx ediconf and gmx solvate tool to prepare solvation system for simulation and at the stage of issuing grompp command for EM , it reports a typical coordinate file mismatch error between solvated.gro and topol.top . surprisingly if I selected any other water model other than TIP4P-Ew at the stage of pdb2gmx, the grompp steps went on right. Since there is no special mentioning in the pdb2gmx -h report or in manual about any special user interference needed to be there in using TIP4P-Ew in pdb2gmx , I wonder why it is behaving like this , I am using the latest version of gromacs-5.0.4. ? Kindly do the needful. With kind regards, Raja -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Abhijit kayal Research Scholar Theoretical Chemistry IIT Kanpur -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Topology file for Fullerene with OPLS_AA force field
it's very much similar creating topology for CNT using g_x2top. You can search mailing list for that. Recently I have published a paper on fullerene water systems. http://www.tandfonline.com/doi/abs/10.1080/08927022.2014.998212#.VTKritzF8wA if you any problem you can contact me. Thanks Abhijit On Wed, Apr 15, 2015 at 11:31 AM, Alex nedoma...@gmail.com wrote: For fullerenes, follow http://www.webcitation.org/66u2xJJ3O and use x2top to build the topology based on OPLSAA. Alex On Wed, Apr 15, 2015 at 12:51 AM, saeed poorasad s_poora...@yahoo.com wrote: Hi Gromacs users , I want to have a system with one C60 and about 1000 water molecules .I tried to use pdb2gmx on C60.pdb but I got fatal error , I think the problem is because of my PDB file .I want to define C-delta atom of the aromatic tryptophan amino acid for C60 carbons and i want to use oplsaa force field. this is a part of my PDB file : HETATM1 CD1 TRP 0 3.341 0.669 0.088 1.00 0.00 CHETATM2 CD1 TRP 0 3.266 -0.548 -0.502 1.00 0.00 CHETATM3 CD1 TRP 0 2.990 -1.662 0.229 1.00 0.00 CHETATM4 CD1 TRP 0 2.750 -0.402 -1.741 1.00 0.00 C I have no experience with GROMACS , so I will be grateful if you can help me . Best ,Saeed. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Abhijit kayal Research Scholar Theoretical Chemistry IIT Kanpur -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] x2top segmentation fault in gromacs 5.0.x, but runs well for 4.0.x, 4.6.x
Hi, I have looked at your carbon nanotube coordinate file (arm.gro). There the terminal C atoms are hydrogen terminated. But you modified the ffnonbonded.itp file with only C atoms. You need to add the parameters for H atoms also both in ffnonbonded.itp and atomname2type.n2t file. Hope this will work. Thanks Abhijit On Fri, Mar 27, 2015 at 5:17 PM, Hao Ren renh...@gmail.com wrote: Hi there, I am trying a MD simulation for carbon nanotubes, but encountered a problem in the preparation of topology file. The coordinates and modified force filed can be found here: https://www.dropbox.com/s/qv4j33sivn56iey/test_x2top.tgz?dl=0 I prepared the modified OPLS/AA force filed as described earlier in this list, post by Dr. Abhijit Kayal ( https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2014-July/090353.html ). A topology file can be generated by the g_x2top module from gromacs 4.0.7 and 4.6.7 using the command line: g_x2top -f arm.gro -o topol.top -ff cnt_oplsaa However, I got a segmentation fault for gromacs 5.0.x, when I use the following command: gmx x2top -f arm.gro -o topol.top -ff cnt_oplsaa I have tried several OS/gcc combinations (centos 6.5/gcc-4.8.2, centos7/gcc-4.8.2, centos6.5/gcc-4.4.7, OSX10.9/homebrew-gcc-4.9.2) with fftw-3.3.4/gcc-4.8.2, all terminated with seg fault. I am not sure whether it comes from my invalid modification of force field or inappropriate compilation of gromacs or an internal bug of the gromacs code. Could anyone kindly help me to locate this problem? Or just test whether you can reproduce the error using your gromacs 5.0.x installation? I appreciate any help and suggestion, Best Regards, /ren PS: The STDOUT looks like the following, = GROMACS: gmx x2top, VERSION 5.0.4 Executable: /opt/gromacs/5.0.4/bin/gmx Library dir: /opt/gromacs/5.0.4/share/gromacs/top Command line: gmx x2top -f arm.gro -o top.top -ff cnt_oplsaa Opening force field file ./cnt_oplsaa.ff/atomname2type.n2t There are 26 name to type translations in file ./cnt_oplsaa.ff Generating bonds from distances... atom 560 There are 3 different atom types in your sample Generating angles and dihedrals from bonds... Segmentation fault (core dumped) == -- Hao Ren, Ph. D. Center for Bioengineering Biotechnology China University of Petroleum Huangdao, Qingdao, Shandong 266580, P. R. China Email: r...@upc.edu.cn Tel: +86-(532) 8698 1135 http://pme.upc.edu.cn/~ren -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Abhijit kayal Research Scholar Theoretical Chemistry IIT Kanpur -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] x2top segmentation fault in gromacs 5.0.x, but runs well for 4.0.x, 4.6.x
If the earlier versions generate the topology then I guess the problem is in your installation. I can't help you much in this regard cause I never tried g_x2top in gromacs 5 version. Thanks Abhijit On Fri, Mar 27, 2015 at 6:11 PM, Hao Ren renh...@gmail.com wrote: Thank you for your prompt reply, Abhijit. I removed all the hydrogen atoms in arm.gro, and changed the number of atoms from 560 to 520, then run the command gmx x2top -f arm.gro -o top.top -ff cnt_oplsaa and, unfortunately, segmentation fault again. It seems that in previous versions (4.6.7 and 4.0.7), g_x2top recognises the hydrogen atoms in the coordinate file (arm.gro) as opls_140: == Hopls_1400.061.008 1C 0.108 == has a single bond with a carbon atom with length 0.108. So I think the seg fault is probably not caused by the hydrogen atoms, (though the using of opls_140 seems problematic ...) /ren -- Hao Ren, Ph. D. Center for Bioengineering Biotechnology China University of Petroleum Huangdao, Qingdao, Shandong 266580, P. R. China Email: r...@upc.edu.cn Tel: +86-(532) 8698 1135 http://pme.upc.edu.cn/~ren On Fri, Mar 27, 2015 at 8:27 PM, abhijit Kayal abhijitchemi...@gmail.com wrote: Hi, I have looked at your carbon nanotube coordinate file (arm.gro). There the terminal C atoms are hydrogen terminated. But you modified the ffnonbonded.itp file with only C atoms. You need to add the parameters for H atoms also both in ffnonbonded.itp and atomname2type.n2t file. Hope this will work. Thanks Abhijit On Fri, Mar 27, 2015 at 5:17 PM, Hao Ren renh...@gmail.com wrote: Hi there, I am trying a MD simulation for carbon nanotubes, but encountered a problem in the preparation of topology file. The coordinates and modified force filed can be found here: https://www.dropbox.com/s/qv4j33sivn56iey/test_x2top.tgz?dl=0 I prepared the modified OPLS/AA force filed as described earlier in this list, post by Dr. Abhijit Kayal ( https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2014-July/090353.html ). A topology file can be generated by the g_x2top module from gromacs 4.0.7 and 4.6.7 using the command line: g_x2top -f arm.gro -o topol.top -ff cnt_oplsaa However, I got a segmentation fault for gromacs 5.0.x, when I use the following command: gmx x2top -f arm.gro -o topol.top -ff cnt_oplsaa I have tried several OS/gcc combinations (centos 6.5/gcc-4.8.2, centos7/gcc-4.8.2, centos6.5/gcc-4.4.7, OSX10.9/homebrew-gcc-4.9.2) with fftw-3.3.4/gcc-4.8.2, all terminated with seg fault. I am not sure whether it comes from my invalid modification of force field or inappropriate compilation of gromacs or an internal bug of the gromacs code. Could anyone kindly help me to locate this problem? Or just test whether you can reproduce the error using your gromacs 5.0.x installation? I appreciate any help and suggestion, Best Regards, /ren PS: The STDOUT looks like the following, = GROMACS: gmx x2top, VERSION 5.0.4 Executable: /opt/gromacs/5.0.4/bin/gmx Library dir: /opt/gromacs/5.0.4/share/gromacs/top Command line: gmx x2top -f arm.gro -o top.top -ff cnt_oplsaa Opening force field file ./cnt_oplsaa.ff/atomname2type.n2t There are 26 name to type translations in file ./cnt_oplsaa.ff Generating bonds from distances... atom 560 There are 3 different atom types in your sample Generating angles and dihedrals from bonds... Segmentation fault (core dumped) == -- Hao Ren, Ph. D. Center for Bioengineering Biotechnology China University of Petroleum Huangdao, Qingdao, Shandong 266580, P. R. China Email: r...@upc.edu.cn Tel: +86-(532) 8698 1135 http://pme.upc.edu.cn/~ren -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Abhijit kayal Research Scholar Theoretical Chemistry IIT Kanpur -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un
[gmx-users] charge vibrating periodically
Dear GROMACS users, Recently I came across a paper where they have mentioned that they placed a vibrating charge near CNT surface. The vibrating charge satisfies the following relation z(t) = Acos(2*pi*f*t+phi), where A is amplitude, f is vibrational frequency and phi is initial phase. So my question is how can I incorporate the vibrating charge in gromacs. In this paper they performed the simulations in gromacs. Any kind of help is highly appreciated. Here is the link of the paper: http://onlinelibrary.wiley.com/doi/10.1002/anie.201408633/abstract Thanks Abhijit -- Abhijit kayal Research Scholar Theoretical Chemistry IIT Kanpur -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] vibrating charge
Dear GROMACS users, Recently I came across a paper where they have mentioned that they placed a vibrating charge near CNT surface. The vibrating charge satisfies the following relation z(t) = Acos(2*pi*f*t+phi), where A is amplitude, f is vibrational frequency and phi is initial phase. So my question is how can I incorporate the vibrating charge in gromacs. In this paper they performed the simulations in gromacs. Any kind of help is highly appreciated. Here is the link of the paper: http://onlinelibrary.wiley.com/doi/10.1002/anie.201408633/abstract Thanks Abhijit -- Abhijit kayal Research Scholar Theoretical Chemistry IIT Kanpur -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] GROMPP COMMAND
Can you tell how you make your topology file for graphene sheet? Because normal way is to do that, first copy the oplsaa.ff file in your working directory, the make the necessary changes in ffnonbonded.itp file and atomname2type.n2t files. Then run g_x2top. The should not give any error. Thanks Abhijit On Mon, Jul 7, 2014 at 10:19 AM, Andy Chao ac...@energiaq.com wrote: Dear GROMACS Users: I have a question regarding using the GROMPP command.. I first used the g_x2top command to convert the *.gro file of a graphene sheet to the *.top file of the graphene sheet by using the forcefield.itp file in the OPLSAA file folder as the following: g_x2top -f graphene.gro -ff oplsaa -o graphene.top and then use the grompp to run energy minimization grompp -f em.mdp -c graphene.gro -p graphene.top -o NPT.ptr why do I get error messages as the following: Program grompp, Version 4.6.5 source code file: /build/buildd/gromacs-4.6.5/src/kernel/topio.c, line: 752 Fatal error: Syntax error - File forcefield.itp, line 24 Last line read: 'opls_071 CG 6 12.01100 0.00 A 3.50E-01 2.92880E-01' Found a second deaults directive. What I don't understand is, why the same forcefield.itp file that allows the *.gro file to be converted to the *.top file has problems when we try to use it to run the grompp file? How should I fix this problem? Thanks! Andy -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Abhijit kayal Research Scholar Theoretical Chemistry IIT Kanpur -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Graphene topology file
Hi Sukirti, Try the following and additionally if you want force and angle constant you can also mention in g_x2top. g_x2top -f gra.pdb -o gra.top -name GRA -nexcl 3 -pbc You have to mention periodic_molecules=yes in the .mdp file. Thanks Abhijit On Fri, Jul 4, 2014 at 1:04 PM, #SUKRITI GUPTA# sukriti...@e.ntu.edu.sg wrote: Hi Abhijit, My g_x2top command is: g_x2top -f gra_2.pdb -o graphene.top -ff oplsaa -name graphene -noparam -pbc The grompp output is: ERROR 4100 [file graphene.top, line 10448]: ; (for all the lines, I have copied here only one line.) No default Ryckaert-Bell. types Excluding 3 bonded neighbours molecule type 'graphene' --- Program grompp, VERSION 4.5.5 Source code file: /build/buildd/gromacs-4.5.5/src/kernel/toppush.c, line: 1987 Fatal error: No such moleculetype SOL For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Thanks Sukriti Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI@N) | Nanyang Technological University Interdisciplinary Graduate School | Office: N1.3-B4-14, 62 Nanyang Drive, Singapore(637459) Tel: (65) 81164191 GMT+8h | Email:sukriti...@e.ntu.edu.sg | Web: erian.ntu.edu.sg From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of abhijit Kayal abhijitchemi...@gmail.com Sent: Friday, July 4, 2014 2:21 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Graphene topology file Hi Sukriti, Can you tell me the g_x2top command you have given and the grompp output. Thanks Abhijit On Fri, Jul 4, 2014 at 10:01 AM, #SUKRITI GUPTA# sukriti...@e.ntu.edu.sg wrote: Dear Justin and Abhijit, Thanks a lot for your help. Now I am able to make the topology file but while doing grompp for energy minimisation its not taking the dihedral values on its own. Regards Sukriti Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI@N ) | Nanyang Technological University Interdisciplinary Graduate School | Office: N1.3-B4-14, 62 Nanyang Drive, Singapore(637459) Tel: (65) 81164191 GMT+8h | Email:sukriti...@e.ntu.edu.sg | Web: erian.ntu.edu.sg From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of abhijit Kayal abhijitchemi...@gmail.com Sent: Thursday, July 3, 2014 6:43 PM To: gmx-us...@gromacs.org; vvcha...@gmail.com Subject: Re: [gmx-users] Graphene topology file Hi Sukriti, Copy the oplsaa.ff directory to your working directory. Then in ffnonbonded.itp file add the following lines.. opls_995 C 612.01100 0.000 A3.4e-01 3.61200e-01 opls_996 C 612.01100 0.000 A3.4e-01 3.61200e-01 opls_997 C 612.01100 0.000 A3.4e-01 3.61200e-01 Then in atomname2type.n2t file add the following lines. Copls_9950 12.011 2C 0.142 C 0.142 Copls_9960 12.011 3C 0.142 C 0.142 C 0.142 Copls_9970 12.011 1C 0.142 Then use g_x2top. This will work. Thanks Abhijit On Thu, Jul 3, 2014 at 3:11 PM, Dr. Vitaly Chaban vvcha...@gmail.com wrote: Graphene topology is like for tube, so C C C ... C ... C C C C C to the N2T file and you are done. Dr. Vitaly V. Chaban On Wed, Jul 2, 2014 at 5:29 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/2/14, 9:56 AM, #SUKRITI GUPTA# wrote: Dear all, I want to simulate graphite in water, for which i am trying to create a topology file for graphite. As its .rtp file cannot be written correctly, i tried to use g_x2top command following the steps given in following tutorial. http://chembytes.wikidot.com/grocnt But I think this tutorial is quite old and hence suitable for older version of gromacs as it still uses FF.dat file. Moreover if i am trying to make a new forcefield directory with name graphite_oplsaa containing the modified files like .n2t,.rtp and .itp, its giving me an error that Could not find force field 'graphite_oplsaa' in current directory, install tree or GMXDATA path. When I try to add this forcefield in original path ie. user/share/gromacs/top, it does not allow me to do that as i am not the administrator. Can anyone please let me know how to create the topology file. I require 3 graphene sheets with pbc. I have created the .pdb file using nanobuilder in vmd. The tutorial is indeed outdated but the logic is fairly sound. You don't
Re: [gmx-users] Graphene topology file
Hi Sukriti, Copy the oplsaa.ff directory to your working directory. Then in ffnonbonded.itp file add the following lines.. opls_995 C 612.01100 0.000 A3.4e-01 3.61200e-01 opls_996 C 612.01100 0.000 A3.4e-01 3.61200e-01 opls_997 C 612.01100 0.000 A3.4e-01 3.61200e-01 Then in atomname2type.n2t file add the following lines. Copls_9950 12.011 2C 0.142 C 0.142 Copls_9960 12.011 3C 0.142 C 0.142 C 0.142 Copls_9970 12.011 1C 0.142 Then use g_x2top. This will work. Thanks Abhijit On Thu, Jul 3, 2014 at 3:11 PM, Dr. Vitaly Chaban vvcha...@gmail.com wrote: Graphene topology is like for tube, so C C C ... C ... C C C C C to the N2T file and you are done. Dr. Vitaly V. Chaban On Wed, Jul 2, 2014 at 5:29 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/2/14, 9:56 AM, #SUKRITI GUPTA# wrote: Dear all, I want to simulate graphite in water, for which i am trying to create a topology file for graphite. As its .rtp file cannot be written correctly, i tried to use g_x2top command following the steps given in following tutorial. http://chembytes.wikidot.com/grocnt But I think this tutorial is quite old and hence suitable for older version of gromacs as it still uses FF.dat file. Moreover if i am trying to make a new forcefield directory with name graphite_oplsaa containing the modified files like .n2t,.rtp and .itp, its giving me an error that Could not find force field 'graphite_oplsaa' in current directory, install tree or GMXDATA path. When I try to add this forcefield in original path ie. user/share/gromacs/top, it does not allow me to do that as i am not the administrator. Can anyone please let me know how to create the topology file. I require 3 graphene sheets with pbc. I have created the .pdb file using nanobuilder in vmd. The tutorial is indeed outdated but the logic is fairly sound. You don't have to modify anything in $GMXLIB (system-wide); you can just create an .n2t file in the working directory and it will override the one at the force field level. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Abhijit kayal Research Scholar Theoretical Chemistry IIT Kanpur -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] how to generate .top file
for gold nano particle you can generate .top file using g_x2top, you have to make necessary changes in ffnonbonded.itp and atomname. n2t files. On Fri, May 23, 2014 at 3:09 PM, Lovika Moudgil lovikamoud...@gmail.comwrote: Hi everyone.. I have a .pdb file with protein and gold slab .Problem is I can generate .top file for my protein with pdb2gmx but I want my slab in the same system .I can generate .gro file for both but what about .top file . Can any body help me with this issue .Thanks in advance. Regards Lovika -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Abhijit kayal Research Scholar Theoretical Chemistry IIT Kanpur -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] (no subject)
Thanks Justin for the help. But if I want to look the dipole auto correlation or hydrogen bond dynamics ... is that possible? On Fri, Feb 28, 2014 at 4:38 PM, Justin Lemkul jalem...@vt.edu wrote: On 2/28/14, 5:38 AM, abhijit Kayal wrote: Dear Gromacs users, My system contained CNT+ water. I have created a dynamically index.ndx file which contain the number of water molecules in each frame inside cnt. Now I want to study the dipole orientation of these water molecules. But I can't select all the groups at a time. From the mailing lists search I came to know that any gromacs analysis tools can't do this. So is there any other way to do these type of analysis. I am using gromacs 4.5.5. You have to analyze each frame individually rather than processing the trajectory in one pass. With a simple shell script, you can loop through the index groups, write out a corresponding frame from the trajectory, then analyze it. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Abhijit kayal Research Scholar Theoretical Chemistry IIT Kanpur -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] CNT in water
when you are creating the forcefield for cnt by g_x2top there you can easily modify the sigma and epsilon value. For that you need to add some values in ffnonbonden.itp file. On Sat, Jan 11, 2014 at 7:07 AM, Justin Lemkul jalem...@vt.edu wrote: On 1/10/14, 6:14 PM, Michelle Aranha wrote: Hi, I am trying to simulate a simple system of CNT in bulk water. The steps that I have completed are: 1. Create a pdb file for CNT. 2. Use editconf to convert to a gro file and define the length of the simulation box, the pbc etc. 3. Create a forcefield folder in my current working directory containing the bonded, nonbonded parameters for CNT molecules. 4. Generate the topology using g_x2top. 5. Solvate the box using genbox. Before proceeding any further with the simulation , I would like to know if I I have to use any combination rules for Carbon water interaction and modify my forcefield file to include this new carbon water interaction potential parameters or does Gromacs take care of it i.e does it automatically update the itp file to include the CNT water interaction while solvating the CNT? Gromacs does whatever the [defaults] directive of the topology tells it. If you're co-opting some existing force field to do this work, then that should already exist. If you're creating the force field from scratch, you will need to tell it all kinds of things, including which type of combination rules are applied. See Chapter 5 of the manual. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Abhijit kayal Research Scholar Theoretical Chemistry IIT Kanpur -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] RDF of Zn_water system using VMD/g_rdf
in g_rdf command you are selecting Zn vs SOL. You first make an index file for only water O atom. Then run g_rdf command and select group O. regarding your second part I am not sure. Can you post the picture of msd? It will be helpful what is going on. On Thu, Jan 9, 2014 at 11:09 PM, M S 18crow...@gmail.com wrote: Dear friends A production run of 2 ns was performed for Zn2+-water system. Now I wanted to generate RDF of (Zn-O) and MSD of Zn ion in water. I followed two methods 1. First using trjconv -f traj.trr -o trajout.gro then opening in vmd and got excellent g(r) for Zn-O with running integration number, n(r). But failed to generate using g_rdf command make_ndx -f traj.trr -s topol.tpr -o index.ndx here i am selecting the whole system as group then g_rdf -n index -o rdf.xvg when it is asking for reference group and 1 more group I am selecting ZN and SOL but when plotting using xmgrace i am geeting multiple peak , one before r_minimum. Puzzling thing is that using same traj.trr, beautiful g(r) for Zn-O was predicted. It will be appreciated if someone catch the fault. second problem (same run for 2 ns) g_msd -f traj.trr -s topol.tpr -o msd.xvg when it is asking for the group selection I am giving ZN but the msd.xvg is found to be noisy and non linear if i read it using xmgrace. Should I have to run the simulation for time than 2 ns. The system size is only 1 ZN and 215 water molecules. Thanks in advance MALI -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Abhijit kayal Research Scholar Theoretical Chemistry IIT Kanpur -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] radial distribution function of fullerene COM and O of water
first run make_ndx to make an index file of water O atom. Next run g_rdf with -com option. this will give you the R.D.F of com of c60 and water O atom. On Mon, Dec 30, 2013 at 10:43 PM, Pratiti Bhadra pratiti.bha...@gmail.comwrote: On Dec 29, 2013 8:51 PM, mali 18crow...@gmail.com wrote: Hi friends Have performed simulation of fullerene and water molecules and calculated free energy of solvation. Now want to calculate the radial distribution function of fullerene COM and O of water molecules. Could you please help how to perform it. Thanks in advance Mali -- View this message in context: http://gromacs.5086.x6.nabble.com/radial-distribution-function-of-fullerene-COM-and-O-of-water-tp5013563.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Abhijit kayal Research Scholar Theoretical Chemistry IIT Kanpur -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
