[gmx-users] Parameters for DMPG and G53a6 force field
Hello, I need parameters for DMPG membrane (G53a6 force field). Does anybody know where I could find a tested parameter set and pdb file? If not, I believe I could construct my own from e.g. Kukol A, Lipid Models for United-Atom Molecular Dynamics Simulations of Proteins, DOI: 10.1021/ct8003468 by merging PG parameters from POPG and the rest of the molecule from DMPC. Thank you, Christopher -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] transmembrane protein simulation
Hi, Yes, g_membed is the right tool for you. Please read the paper Wolf et al, J Comp Chem, 31 (2010) 2169-2174. You will find a detailed description of the insertion method and a quick manual. It will save you a lot of headache. Regards, Christopher 2011/1/24 Mohana lakshmi mohanaa.bioi...@gmail.com Dear all I am trying to run simulation of transmembrane protein, i am looking for better ways to setup protein with lipid membrane. initially i used VMD to insert protein with lipid membrane but it did not come out well, i got errors while running position restraint. i read about g_membed tool in gromacs, is it helpful for setting up transmembrane proteins also? Is there any other better ways to insert protein perfectly into the membrane? Please help me to overcome this problem. Thanks and regards -- Mohanalakshmi N -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Installing gromacs in Red hat E5
I'd also suggest to install the newest version 4.5.2. Chris 2010/11/9 Kamalesh Roy roy.kamales...@gmail.com Dear all, Can anybody tell me the the specification of installation of gromacs 4.5.1 in Red Hat E5 platform. GCC package works good here or any other option I have to think of. Thank you kamalesh Roy Department of Biophysics, Molecular Biology and Bioinformatics University of Calcutta, India -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Using mdrun -rerun to get energy values
Hi, You need to use md integrator for -rerun to work. Good luck, Chris 2010/11/6 Martin Kamp Jensen martin.kamp.jen...@gmail.com Hello, Hopefully someone can help me understand how to use the mdrun -rerun functionality, because currently I am confused. I would like to be able to look up potential energy values for a number of conformations by calling mdrun -rerun once. The idea to use mdrun -rerun is from advice given to me by Mark Abraham on the gmx-developers list ( http://lists.gromacs.org/pipermail/gmx-developers/2010-September/004731.html and http://lists.gromacs.org/pipermail/gmx-developers/2010-October/004770.html ): You want GROMACS to find the energy of a potentially infinite set of coordinates that appear magically, and that is what mdrun -rerun does. The elegant way to do that is to write your series of conformations to a pseudo-trajectory (in whichever of GROMACS many trajectory formats is convenient to you), and then invoke mdrun -rerun on that trajectory with a suitable .tpr. Then you either parse the .log file or the output .edr file for the energies. I wanted to find out how this works so I have been experimenting. I started out by looking at the Peptide tutorial at http://manual.gromacs.org/current/online/speptide.html. I used three different mdp files (integrator = steep, nsteps = 0, 1, 2). This gave me three conformations and their energy values. For testing purposes I then wanted to get the energy values for those three conformations using mdrun -rerun (and since I already have the correct energy values it is easy to verify the results). First, I created a trajectory by concatenating the three conformations (gro files) into one gro file (which is okay according to http://manual.gromacs.org/current/online/gro.html: gro files can be used as trajectory by simply concatenating files). I then used an mdp file with integrator = steep and nsteps = 0 indicating that I just want the energy value (listed in the output, in the log file or by using g_energy). Now, by using mdrun -s tpr file -rerun gro trajectory file I only get the energy value for the first conformation listed in the gro file used to create the tpr file. The -rerun option does not seem to have any effect at all. I used the following commands three times to create three different conformations (one conf_mdrun.gro file for each time) with different energy values. I am just setting nsteps to 0, 1, or 2 (integrator = steep) in em.mdp. pdb2gmx -f speptide -o conf_pdb2gmx -p top_pdb2gmx -i top_pdb2gmx EOF 1 1 EOF editconf -f conf_pdb2gmx -o conf_editconf -d 0.5 genbox -cp conf_editconf -cs -p top_pdb2gmx -o conf_genbox mv top_pdb2gmx.top top_genbox.top mv #top_pdb2gmx.top.1# top_pdb2gmx.top grompp -f em -po em_grompp -c conf_genbox -p top_genbox -o em_grompp mdrun -s em_grompp -o mdrun -c conf_mdrun -e mdrun -g mdrun I was hoping the following would give me the three energy values for the three conformations in 2+1+0.gro, which is the concatenation of the three conf_mdrun.gro files from before. However, I just get the energy value from the first conformation in the file. Using the -rerun option does not make a difference (I can put whatever after -rerun, even files that do not exist, without any effect). grompp -f em -po em_grompp -c gro/2+1+0 -p top_genbox -o em_grompp mdrun -s em_grompp.tpr -rerun gro/2+1+0.gro Regards, Martin. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Using mdrun -rerun to get energy values
Hi Martin, Well, I was browsing the source code just yesterday cause I also noticed that with steep integrator mdrun does not notice -rerun presence. And it turned out that in do_steep() no one cares if -rerun is on. And if you think for a moment what it does, it makes sense. However, it would be good to add a check in the future releases so that gmx_fatal() is called in case someone combines -rerun with integrators from minimize.c. I'm happy that I was helpful. Chris 2010/11/6 Martin Kamp Jensen martin.kamp.jen...@gmail.com Hi Chris, On Sat, Nov 6, 2010 at 5:58 PM, Krzysztof Mlynarczyk mitomas...@gmail.com wrote: Hi, You need to use md integrator for -rerun to work. Aha, now it seems to work. Thanks! I am just sad that I did not find that information. According to http://manual.gromacs.org/current/online/mdrun.html With -rerun an input trajectory can be given for which forces and energies will be (re)calculated. Neighbor searching will be performed for every frame, unless nstlist is zero (see the .mdp file). Good luck, Chris 2010/11/6 Martin Kamp Jensen martin.kamp.jen...@gmail.com Hello, Hopefully someone can help me understand how to use the mdrun -rerun functionality, because currently I am confused. I would like to be able to look up potential energy values for a number of conformations by calling mdrun -rerun once. The idea to use mdrun -rerun is from advice given to me by Mark Abraham on the gmx-developers list ( http://lists.gromacs.org/pipermail/gmx-developers/2010-September/004731.html and http://lists.gromacs.org/pipermail/gmx-developers/2010-October/004770.html ): You want GROMACS to find the energy of a potentially infinite set of coordinates that appear magically, and that is what mdrun -rerun does. The elegant way to do that is to write your series of conformations to a pseudo-trajectory (in whichever of GROMACS many trajectory formats is convenient to you), and then invoke mdrun -rerun on that trajectory with a suitable .tpr. Then you either parse the .log file or the output .edr file for the energies. I wanted to find out how this works so I have been experimenting. I started out by looking at the Peptide tutorial at http://manual.gromacs.org/current/online/speptide.html. I used three different mdp files (integrator = steep, nsteps = 0, 1, 2). This gave me three conformations and their energy values. For testing purposes I then wanted to get the energy values for those three conformations using mdrun -rerun (and since I already have the correct energy values it is easy to verify the results). First, I created a trajectory by concatenating the three conformations (gro files) into one gro file (which is okay according to http://manual.gromacs.org/current/online/gro.html: gro files can be used as trajectory by simply concatenating files). I then used an mdp file with integrator = steep and nsteps = 0 indicating that I just want the energy value (listed in the output, in the log file or by using g_energy). Now, by using mdrun -s tpr file -rerun gro trajectory file I only get the energy value for the first conformation listed in the gro file used to create the tpr file. The -rerun option does not seem to have any effect at all. I used the following commands three times to create three different conformations (one conf_mdrun.gro file for each time) with different energy values. I am just setting nsteps to 0, 1, or 2 (integrator = steep) in em.mdp. pdb2gmx -f speptide -o conf_pdb2gmx -p top_pdb2gmx -i top_pdb2gmx EOF 1 1 EOF editconf -f conf_pdb2gmx -o conf_editconf -d 0.5 genbox -cp conf_editconf -cs -p top_pdb2gmx -o conf_genbox mv top_pdb2gmx.top top_genbox.top mv #top_pdb2gmx.top.1# top_pdb2gmx.top grompp -f em -po em_grompp -c conf_genbox -p top_genbox -o em_grompp mdrun -s em_grompp -o mdrun -c conf_mdrun -e mdrun -g mdrun I was hoping the following would give me the three energy values for the three conformations in 2+1+0.gro, which is the concatenation of the three conf_mdrun.gro files from before. However, I just get the energy value from the first conformation in the file. Using the -rerun option does not make a difference (I can put whatever after -rerun, even files that do not exist, without any effect). grompp -f em -po em_grompp -c gro/2+1+0 -p top_genbox -o em_grompp mdrun -s em_grompp.tpr -rerun gro/2+1+0.gro Regards, Martin. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http
Re: [gmx-users] The grompp problem!! (Urgently)
If this is the tutorial I have in front of my eyes, then the problem is that order of force fields changed and gromacs force field you are told to choose is no longer under 0 as it is deprecated. 0 is ffG43a1, where this atom type is not present anymore. Good luck, Chris 2010/7/22 Yuranat Saikatikorn sug...@gmail.com I am doing the Drug-enzyme tutorial. I also generated the drg.itp, drg.gro files using PRODRG server. However, when I use the grompp command before the energy minimization I face some error A fatal error was shown: atom types CR61 not found The atom type CR61 is presented in the drg.itp file that I included to .top file before using grompp. What should I do to get through this error? Many thanks Yuranat, -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Help for running gromacs
Please post more details including the following: - What is the exact command line? - What group do you select as a continuous solvent? I know it might sound weird to ask this but what I learned while teaching students is that these questions really should be asked when there are problems. - Which version of Gromacs are you using? 2010/5/3 priyanka panwar priyankapanwa...@gmail.com I am using Gromacs for Simulation of Insulin.I have generated most of the files but unable to generate the ions.pdb file.The system is becoming idle after the Selection command. A line on the command prompt appears as replacing solvent molecule with Na and remains as such for many hours. Is this step really takes too much time or I am doing something wrong. Thanks -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] MARTINI-CG updated web site
I wish G96 force fields had a similar website with so much useful information. It would be good if authors posted anything on the forum cause it's completely empty right now. 2010/1/26 XAvier Periole x.peri...@rug.nl Dears, the MARTINI CG force field web site has been remodeled. It now includes FAQs, tutorials, a forum and much more ... http://md.chem.rug.nl/cgmartini Enjoy. -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Lipid parameters for GROMOS96 force fields
Hi, I already have both your publication and supplementary material from your website. The files were also submitted to Gromacs user contribution section: http://www.gromacs.org/@api/deki/files/23/=LipidsForGro96_53a6.zip Have you noticed anything suspicious in alpha helix behaviour in G53a6 force field? Christopher 2010/1/21 Kukol, Andreas a.ku...@herts.ac.uk Hi, Lipid parameters for Gromos96 53a6 are available based on the publication Kukol, A., 2009. Lipid models for united-atom molecular dynamics simulations of proteins. J. Chem. Theor. Comput.,5(3), 615-626. Unfortunately, I did not manage yet to upload it on the new Gromacs website. Please contact me off the list for the itp-files for DPPC, DMPC, POPC and POPG for 53a6 forcefield. Andreas -Original Message- From: gmx-users-boun...@gromacs.org [mailto: gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: 21 January 2010 01:36 To: Discussion list for GROMACS users Subject: Re: [gmx-users] Lipid parameters for GROMOS96 force fields Justin A. Lemkul wrote: Krzysztof Mlynarczyk wrote: Hello, On Peter Tieleman's website we can find topologies for various popular lipids. However those seem to be valid for the deprecated GROMOS87 force field. The g96_lipids.itp file is still unavailable. I'd like to run a simulation of 7TM protein embedded into POPC membrane. G43a2x seems to be a reasonable choice for this purpose. I still need the parameters for my lipids. I am aware that combining parameters from different force fields might lead to a disaster, that's why I want to ask you: 1. Do you know any papers where POPC membrane and G43a2 force field was used? I've not seen one, because it has been known for some time that early Gromos96 parameter sets did not reproduce long alkyl chain properties particularly well. Quick amendment - modifications to 43a2 and 45a3 have been made to better reproduce lipid properties. Both are available for download on the Gromacs site and you can probably track down the references, as well. Sorry, read that one wrong the first time :) -Justin 2. If not, is there any way to derive the proper parameters for the force field of my choice using the lipid parameters from Peter Tieleman's website or e.g. the parameters published by Andreas Kukol for G53a6? I don't see why you need to do such reverse engineering. The Kukol parameters for lipids under 53a6 can be directly combined with a G53a6 protein without any issues; I believe that was the purpose of the whole new derivation :) As an aside, you are quite right that multiple force fields within the same simulation is incorrect. However, the Berger lipid parameters may be an exception to this rule, since they are really a hybridized version of OPLS-UA and Gromos87 parameters (some of which were modified anyway), so they really don't belong to any one particular force field. The Berger/G87 combination is widely used, but essentially amounts to the following: lipid interactions are Berger-Berger or OPLS-OPLS interactions, while protein-lipid interations are Berger-G87, and protein-protein interactions are G87-G87. You can see quite quickly why things become complicated! Based on a discussion I had with Dr. Tieleman, it seems to be reasonable to use the G96 parameter set of your choice in conjunction with lipid.itp (Berger lipids), although other approaches may be more rigorously correct (pure G96 parameters such as those by Kukol, pure OPLS recently derived by Ulmschneider, or the modifications to the Berger parameters from the Tieleman group, to name a few). If you want to use a G96-lipid.itp combination, I created a tutorial that teaches you how to build the system and properly prepare the topology. It is linked from the Tutorials page of the Gromacs site. -Justin Thank you in advance, Christopher -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@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
Re: [gmx-users] Lipid parameters for GROMOS96 force fields
2010/1/21 Justin A. Lemkul jalem...@vt.edu Krzysztof Mlynarczyk wrote: 2. If not, is there any way to derive the proper parameters for the force field of my choice using the lipid parameters from Peter Tieleman's website or e.g. the parameters published by Andreas Kukol for G53a6? I don't see why you need to do such reverse engineering. The Kukol parameters for lipids under 53a6 can be directly combined with a G53a6 protein without any issues; I believe that was the purpose of the whole new derivation :) I received a message that G53a6 is beta-sheet biased and alpha helices do not perform as well as they should. My protein contains 7 transmembrane helices, that's why I'm worried. I know that there are changes between parameter sets both in non-bonded and bonded terms and one rtp entry will probably not work well when pasted into a different force field from the same family. G96 family uses symbols like gd_5 that are substituted by appropriate parameters later through the use of preprocessor. While it is possible to find that gd_5 is the same as gd_15 in another version of G96 and substitute those symbols in topologies, the changes in non bonded parameters still can spoil what was working well elsewhere. That's why I was also asking for some checked and ready-to-use topologies for a particular force field. As an aside, you are quite right that multiple force fields within the same simulation is incorrect. However, the Berger lipid parameters may be an exception to this rule, since they are really a hybridized version of OPLS-UA and Gromos87 parameters (some of which were modified anyway), so they really don't belong to any one particular force field. The Berger/G87 combination is widely used, but essentially amounts to the following: lipid interactions are Berger-Berger or OPLS-OPLS interactions, while protein-lipid interations are Berger-G87, and protein-protein interactions are G87-G87. You can see quite quickly why things become complicated! Based on a discussion I had with Dr. Tieleman, it seems to be reasonable to use the G96 parameter set of your choice in conjunction with lipid.itp (Berger lipids), although other approaches may be more rigorously correct (pure G96 parameters such as those by Kukol, pure OPLS recently derived by Ulmschneider, or the modifications to the Berger parameters from the Tieleman group, to name a few). If you want to use a G96-lipid.itp combination, I created a tutorial that teaches you how to build the system and properly prepare the topology. It is linked from the Tutorials page of the Gromacs site. I found this tutorial earlier and was also in doubt if this approach was correct. But if it works, perhaps I should give it a try. I gotta make a _good_ decision in the end... Christopher -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Lipid parameters for GROMOS96 force fields
Hello, I'm very happy that so many people contributed to the subject of the (in)validity of using G53a6 for alpha helical proteins. Thank you for the links. I know now that I certainly should use a different force field from the GROMOS96 family, which maintains alpha helices where they should be and there are tested parameters for the lipid of my choice, POPC. I could merge lipid.itp with this force field's files and use a ready topology - that's one option... Christopher 2010/1/21 Tsjerk Wassenaar tsje...@gmail.com Hi, Well, we have compared the G53a5/6 force field with the 43a2 one and found consistently larger radii of gyration and higher RMSDs, suggesting decreased stability. There's a thorough account of it in my thesis ( http://dissertations.ub.rug.nl/FILES/faculties/science/2006/t.a.wassenaar/04emb_c4.pdf ) and it's been published in JPCB in 2007 (DOI: 10.1021/jp068580v). Cheers, Tsjerk On Thu, Jan 21, 2010 at 2:24 PM, XAvier Periole x.peri...@rug.nl wrote: The instability of helices with the G53a6 force field is definitely real and unfortunately not documented. Some people are working on it ... I would advise to be very carefull in interpreting results with this FF. XAvier. On Jan 21, 2010, at 2:13 PM, Justin A. Lemkul wrote: Krzysztof Mlynarczyk wrote: 2010/1/21 Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu Krzysztof Mlynarczyk wrote: 2. If not, is there any way to derive the proper parameters for the force field of my choice using the lipid parameters from Peter Tieleman's website or e.g. the parameters published by Andreas Kukol for G53a6? I don't see why you need to do such reverse engineering. The Kukol parameters for lipids under 53a6 can be directly combined with a G53a6 protein without any issues; I believe that was the purpose of the whole new derivation :) I received a message that G53a6 is beta-sheet biased and alpha helices do not perform as well as they should. My protein contains 7 transmembrane helices, that's why I'm worried. Is this published somewhere? That would be important information. Perhaps this is the case for model peptides or short fragments, but I have certainly done a number of simulations using 53a6 with well-folded globular proteins and I do not see any such instability (i.e., alpha-beta conversion or unwinding of alpha-helices). I do believe it is possible in certain scenarios, but I don't know that a large 7TM protein like yours would suffer adversely. I know that there are changes between parameter sets both in non-bonded and bonded terms and one rtp entry will probably not work well when pasted into a different force field from the same family. G96 family uses symbols like gd_5 that are substituted by appropriate parameters later through the use of preprocessor. While it is possible to find that gd_5 is the same as gd_15 in another version of G96 and substitute those symbols in topologies, the changes in non bonded parameters still can spoil what was working well elsewhere. That's why I was also asking for some checked and ready-to-use topologies for a particular force field. Many of the bonded parameters carry over between force fields, but certainly new entries were created between 43a2 and 53a6, so yes, some re-working would likely be necessary. There is a lipid 43a2 parameter set on the User Contribution site, like I said before, I just don't know if there is a reference for it. As an aside, you are quite right that multiple force fields within the same simulation is incorrect. However, the Berger lipid parameters may be an exception to this rule, since they are really a hybridized version of OPLS-UA and Gromos87 parameters (some of which were modified anyway), so they really don't belong to any one particular force field. The Berger/G87 combination is widely used, but essentially amounts to the following: lipid interactions are Berger-Berger or OPLS-OPLS interactions, while protein-lipid interations are Berger-G87, and protein-protein interactions are G87-G87. You can see quite quickly why things become complicated! Based on a discussion I had with Dr. Tieleman, it seems to be reasonable to use the G96 parameter set of your choice in conjunction with lipid.itp (Berger lipids), although other approaches may be more rigorously correct (pure G96 parameters such as those by Kukol, pure OPLS recently derived by Ulmschneider, or the modifications to the Berger parameters from the Tieleman group, to name a few). If you want to use a G96-lipid.itp combination, I created a tutorial that teaches you how to build the system and properly prepare the topology. It is linked from the Tutorials page of the Gromacs site. I found this tutorial earlier and was also in doubt if this approach was correct
Re: [gmx-users] Lipid parameters for GROMOS96 force fields
Thank you!!! The evidence presented in this paper is stunning. It also stresses the importance of using the electrostatics treatment that was originally used for development of a particular force field, e.g. reaction field in case of G96 - the popular PME in connection with G53a6 results in even stronger beta sheet bias. This way using this force field is out of the question, unless until corrections are made and tested. I need a different solution for my problem. Christopher 2010/1/21 Erik Marklund er...@xray.bmc.uu.se It is documented. Have a look at this one: Dirk Matthes and Bert L. de Groot. Secondary structure propensities in peptide folding simulations: A systematic comparison of molecular mechanics interaction schemes. Biophys. J. 97:599-608 (2009) Erik XAvier Periole skrev: The instability of helices with the G53a6 force field is definitely real and unfortunately not documented. Some people are working on it ... I would advise to be very carefull in interpreting results with this FF. XAvier. On Jan 21, 2010, at 2:13 PM, Justin A. Lemkul wrote: Krzysztof Mlynarczyk wrote: 2010/1/21 Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu Krzysztof Mlynarczyk wrote: 2. If not, is there any way to derive the proper parameters for the force field of my choice using the lipid parameters from Peter Tieleman's website or e.g. the parameters published by Andreas Kukol for G53a6? I don't see why you need to do such reverse engineering. The Kukol parameters for lipids under 53a6 can be directly combined with a G53a6 protein without any issues; I believe that was the purpose of the whole new derivation :) I received a message that G53a6 is beta-sheet biased and alpha helices do not perform as well as they should. My protein contains 7 transmembrane helices, that's why I'm worried. Is this published somewhere? That would be important information. Perhaps this is the case for model peptides or short fragments, but I have certainly done a number of simulations using 53a6 with well-folded globular proteins and I do not see any such instability (i.e., alpha-beta conversion or unwinding of alpha-helices). I do believe it is possible in certain scenarios, but I don't know that a large 7TM protein like yours would suffer adversely. I know that there are changes between parameter sets both in non-bonded and bonded terms and one rtp entry will probably not work well when pasted into a different force field from the same family. G96 family uses symbols like gd_5 that are substituted by appropriate parameters later through the use of preprocessor. While it is possible to find that gd_5 is the same as gd_15 in another version of G96 and substitute those symbols in topologies, the changes in non bonded parameters still can spoil what was working well elsewhere. That's why I was also asking for some checked and ready-to-use topologies for a particular force field. Many of the bonded parameters carry over between force fields, but certainly new entries were created between 43a2 and 53a6, so yes, some re-working would likely be necessary. There is a lipid 43a2 parameter set on the User Contribution site, like I said before, I just don't know if there is a reference for it. As an aside, you are quite right that multiple force fields within the same simulation is incorrect. However, the Berger lipid parameters may be an exception to this rule, since they are really a hybridized version of OPLS-UA and Gromos87 parameters (some of which were modified anyway), so they really don't belong to any one particular force field. The Berger/G87 combination is widely used, but essentially amounts to the following: lipid interactions are Berger-Berger or OPLS-OPLS interactions, while protein-lipid interations are Berger-G87, and protein-protein interactions are G87-G87. You can see quite quickly why things become complicated! Based on a discussion I had with Dr. Tieleman, it seems to be reasonable to use the G96 parameter set of your choice in conjunction with lipid.itp (Berger lipids), although other approaches may be more rigorously correct (pure G96 parameters such as those by Kukol, pure OPLS recently derived by Ulmschneider, or the modifications to the Berger parameters from the Tieleman group, to name a few). If you want to use a G96-lipid.itp combination, I created a tutorial that teaches you how to build the system and properly prepare the topology. It is linked from the Tutorials page of the Gromacs site. I found this tutorial earlier and was also in doubt if this approach was correct. But if it works, perhaps I should give it a try. I gotta make a _good_ decision in the end... As do we all :) My work with G53a6+Berger has thus far been quite reliable, from everything I can measure, but that certainly does not preclude the possibility (even
[gmx-users] Lipid parameters for GROMOS96 force fields
Hello, On Peter Tieleman's website we can find topologies for various popular lipids. However those seem to be valid for the deprecated GROMOS87 force field. The g96_lipids.itp file is still unavailable. I'd like to run a simulation of 7TM protein embedded into POPC membrane. G43a2x seems to be a reasonable choice for this purpose. I still need the parameters for my lipids. I am aware that combining parameters from different force fields might lead to a disaster, that's why I want to ask you: 1. Do you know any papers where POPC membrane and G43a2 force field was used? 2. If not, is there any way to derive the proper parameters for the force field of my choice using the lipid parameters from Peter Tieleman's website or e.g. the parameters published by Andreas Kukol for G53a6? Thank you in advance, Christopher -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Angle between normal of rings at same molecule
I'm not sure if this can be done with any of the gromacs tools, but using the linalg module from numpy library will help you. But be aware that a flip by 180 degrees is meaningful for you, but undistinguishable for the mathematical procedure. This issue can be more or less easily solved depending on your system. Christopher 2010/1/11 Eudes Fileti fil...@ufabc.edu.br: Dear gmx-users, I have a molecule with two rings and would like to calculate the angle between the normal vector of these rings. Anyone have idea of how this can be done? eef __ Eudes Eterno Fileti Centro de Ciências Naturais e Humanas Universidade Federal do ABC — CCNH Av. dos Estados, 5001 Santo André - SP - Brasil CEP 09210-971 +55.11.4437-0196 http://fileti.ufabc.edu.br -- gmx-users mailing list gmx-us...@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
