Re: [gmx-users] converting amber distributed parameters to gromacs.
ffamber.cnsm.csulb.edu/amb2gmx.pl On 11/07/2012 09:45 AM, Rajiv Gandhi wrote: Dear Gromacs user, I have found the parameters file for my ligand which is available in AMBER distribution parameter database, Could you advice me how do i use them in running over MD in gromacs? Thanks in advance, Regards Raju -- 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] Polarisation model
Dear all, I am a new Gromacs user. In the past I used AMBER, but because of performance and technical reason I want to switch to Gromacs. Actually, I have one big problem namely polarisation. In AMBER I used the atomic point dipole model but this one is not implemented in Gromacs (please correct me if I am wrong). Are there any experienced data which compare the two models, atomic point dipole and shell?? Kind regards, Volker -- Volker Lesch Institut für physikalische Chemie Westfälische Wilhelms-Universität Münster Corrensstrasse 28/30 48149 Münster Phone: +49-(0)-251-83-29180 Email: volkerle...@uni-muenster.de -- 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] converting amber distributed parameters to gromacs.
Could you please tell how do i use this script over amber file? Thanks. On Wed, Nov 7, 2012 at 5:58 PM, Felipe Pineda, PhD luis.pinedadecas...@lnu.se wrote: ffamber.cnsm.csulb.edu/**amb2gmx.plhttp://ffamber.cnsm.csulb.edu/amb2gmx.pl On 11/07/2012 09:45 AM, Rajiv Gandhi wrote: Dear Gromacs user, I have found the parameters file for my ligand which is available in AMBER distribution parameter database, Could you advice me how do i use them in running over MD in gromacs? Thanks in advance, Regards Raju -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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] converting amber distributed parameters to gromacs.
There is not too much to say: the script is self-explanatory. Look also: http://www.gromacs.org/Documentation/Terminology/Force_Fields/AMBER?highlight=antechamber On 11/07/2012 10:27 AM, Rajiv Gandhi wrote: Could you please tell how do i use this script over amber file? Thanks. On Wed, Nov 7, 2012 at 5:58 PM, Felipe Pineda, PhD luis.pinedadecas...@lnu.se wrote: ffamber.cnsm.csulb.edu/**amb2gmx.plhttp://ffamber.cnsm.csulb.edu/amb2gmx.pl On 11/07/2012 09:45 AM, Rajiv Gandhi wrote: Dear Gromacs user, I have found the parameters file for my ligand which is available in AMBER distribution parameter database, Could you advice me how do i use them in running over MD in gromacs? Thanks in advance, Regards Raju -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- +---+ | Luis Felipe Pineda De Castro, PhD | | Computational Chemist - Postdoc | | Computational Chemistry and | | Biochemistry Laboratory | | School of Natural Sciences| | Linnaeus University | | SE-391 82 Kalmar | | Norrgård, room 311| | Sweden - Sverige | | Phone: ++46-480-44 6329 | | Mobile: ++46-76-8420572 | | E-Mail: luis.pinedadecas...@lnu.se| | Web:lnu.se| +---+ -- 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] Polarisation model
On 2012-11-07 10:21, Volker Lesch wrote: Dear all, I am a new Gromacs user. In the past I used AMBER, but because of performance and technical reason I want to switch to Gromacs. Actually, I have one big problem namely polarisation. In AMBER I used the atomic point dipole model but this one is not implemented in Gromacs (please correct me if I am wrong). Are there any experienced data which compare the two models, atomic point dipole and shell?? Kind regards, Volker This is not implemented. The shell model works but with limited functionality, such that the Charmm model does not work completely. It would be interesting to have such a comparison although I expect few significant differences. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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] Polarisation model
On 11/07/2012 11:19 AM, David van der Spoel wrote: On 2012-11-07 10:21, Volker Lesch wrote: Dear all, I am a new Gromacs user. In the past I used AMBER, but because of performance and technical reason I want to switch to Gromacs. Actually, I have one big problem namely polarisation. In AMBER I used the atomic point dipole model but this one is not implemented in Gromacs (please correct me if I am wrong). Are there any experienced data which compare the two models, atomic point dipole and shell?? Kind regards, Volker This is not implemented. The shell model works but with limited functionality, such that the Charmm model does not work completely. It would be interesting to have such a comparison although I expect few significant differences. Hallo, thanks for this reply. So the shell model only works for simple systems like water. Is this correct? What are the exact limitations? Kind regards, Volker -- Volker Lesch Institut für physikalische Chemie Westfälische Wilhelms-Universität Münster Corrensstrasse 28/30 48149 Münster Phone: +49-(0)-251-83-29180 Email: volkerle...@uni-muenster.de -- 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] Polarisation model
On 2012-11-07 11:24, Volker Lesch wrote: On 11/07/2012 11:19 AM, David van der Spoel wrote: On 2012-11-07 10:21, Volker Lesch wrote: Dear all, I am a new Gromacs user. In the past I used AMBER, but because of performance and technical reason I want to switch to Gromacs. Actually, I have one big problem namely polarisation. In AMBER I used the atomic point dipole model but this one is not implemented in Gromacs (please correct me if I am wrong). Are there any experienced data which compare the two models, atomic point dipole and shell?? Kind regards, Volker This is not implemented. The shell model works but with limited functionality, such that the Charmm model does not work completely. It would be interesting to have such a comparison although I expect few significant differences. Hallo, thanks for this reply. So the shell model only works for simple systems like water. Is this correct? What are the exact limitations? Kind regards, Volker In Charmm there are additional terms for screening like the Thole potential, which is implemented in gmx but not really debugged thoroughly yet. However, the Charmm people also use some kind of non-bonded screening that is not implemented. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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] Protein at given pH
On 11/7/12 4:19 AM, Steven Neumann wrote: Dear Gmx Users, I am trying to simulate protein-ligand interactions at specific pH=5. I processed my protein.pdb into the H++. As I see from th titration curve of the entire molecule it appears that at pH=5 the total charge should be equal to 2. When I process the obtained pdb from the server to pdb2gmx using -ignh I get the total charge of -3. Can anyone explain me this? pdb2gmx chooses protonation states based on the assumption that you're working at neutral pH. If you want some alternate protonation state for certain residues, you have to choose them yourself using the various options that pdb2gmx provides for this purpose. In terms of small molecules how can I get parameters at specific pH? I am using Charmm and parachem.org does not support pH changes. Can anyone advise? pKa values for most common groups should make the protonation state at a given pH fairly straightforward, otherwise you need to calculate the pKa's in some way and adjust the molecule's protonation accordingly. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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/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] Protein at given pH
On Wed, Nov 7, 2012 at 11:56 AM, Justin Lemkul jalem...@vt.edu wrote: On 11/7/12 4:19 AM, Steven Neumann wrote: Dear Gmx Users, I am trying to simulate protein-ligand interactions at specific pH=5. I processed my protein.pdb into the H++. As I see from th titration curve of the entire molecule it appears that at pH=5 the total charge should be equal to 2. When I process the obtained pdb from the server to pdb2gmx using -ignh I get the total charge of -3. Can anyone explain me this? pdb2gmx chooses protonation states based on the assumption that you're working at neutral pH. If you want some alternate protonation state for certain residues, you have to choose them yourself using the various options that pdb2gmx provides for this purpose. Thank you Justin. So do not understand why this server produce pdb file which is redundant as you have to use -his -glu etc. flags anyway. According to pK - this server predicts pK for each residue and when my pH pKa it is protonated, otherwise it is deprotonated, right? How about pH = pKa ? Steven In terms of small molecules how can I get parameters at specific pH? I am using Charmm and parachem.org does not support pH changes. Can anyone advise? pKa values for most common groups should make the protonation state at a given pH fairly straightforward, otherwise you need to calculate the pKa's in some way and adjust the molecule's protonation accordingly. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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/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] Protein at given pH
On 11/7/12 7:10 AM, Steven Neumann wrote: On Wed, Nov 7, 2012 at 11:56 AM, Justin Lemkul jalem...@vt.edu wrote: On 11/7/12 4:19 AM, Steven Neumann wrote: Dear Gmx Users, I am trying to simulate protein-ligand interactions at specific pH=5. I processed my protein.pdb into the H++. As I see from th titration curve of the entire molecule it appears that at pH=5 the total charge should be equal to 2. When I process the obtained pdb from the server to pdb2gmx using -ignh I get the total charge of -3. Can anyone explain me this? pdb2gmx chooses protonation states based on the assumption that you're working at neutral pH. If you want some alternate protonation state for certain residues, you have to choose them yourself using the various options that pdb2gmx provides for this purpose. Thank you Justin. So do not understand why this server produce pdb file which is redundant as you have to use -his -glu etc. flags anyway. According to pK - this server predicts pK for each residue and when my pH pKa it is protonated, otherwise it is deprotonated, right? How about pH = pKa ? If you're using the H++ server, it has no connection to Gromacs in any way. Your command line uses -ignh, so any hope of guessing the protonation state from the input is lost and thus you have to use interactive selection to counteract that effect or otherwise hope that all the atomic nomenclature is right so that pdb2gmx doesn't complain too much. If pH = pKa, then your life is tougher. In solution, 50% of the residues in the protein molecules will be protonated, 50% deprotonated. You may have to model both protonation states if this is the case. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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/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] Protein at given pH
On Wed, Nov 7, 2012 at 12:20 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/7/12 7:10 AM, Steven Neumann wrote: On Wed, Nov 7, 2012 at 11:56 AM, Justin Lemkul jalem...@vt.edu wrote: On 11/7/12 4:19 AM, Steven Neumann wrote: Dear Gmx Users, I am trying to simulate protein-ligand interactions at specific pH=5. I processed my protein.pdb into the H++. As I see from th titration curve of the entire molecule it appears that at pH=5 the total charge should be equal to 2. When I process the obtained pdb from the server to pdb2gmx using -ignh I get the total charge of -3. Can anyone explain me this? pdb2gmx chooses protonation states based on the assumption that you're working at neutral pH. If you want some alternate protonation state for certain residues, you have to choose them yourself using the various options that pdb2gmx provides for this purpose. Thank you Justin. So do not understand why this server produce pdb file which is redundant as you have to use -his -glu etc. flags anyway. According to pK - this server predicts pK for each residue and when my pH pKa it is protonated, otherwise it is deprotonated, right? How about pH = pKa ? If you're using the H++ server, it has no connection to Gromacs in any way. Your command line uses -ignh, so any hope of guessing the protonation state from the input is lost and thus you have to use interactive selection to counteract that effect or otherwise hope that all the atomic nomenclature is right so that pdb2gmx doesn't complain too much. If pH = pKa, then your life is tougher. In solution, 50% of the residues in the protein molecules will be protonated, 50% deprotonated. You may have to model both protonation states if this is the case. -Justin Thank you for this! Steven -- Justin A. Lemkul, Ph.D. Research Scientist 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/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] Protein at given pH
Hi, I've used the H++ server myself at times. My experience is that it's rather sensitive to the very fine detail of the input structure in some cases. I've had situations where H++ suggest one protonation state, then a short md simulation takes the system to a slightly different conformation that seem more prevalent but that yields another protonation state if sent to H++ again. Use all biochemical knowledge that you can muster to check that the output makes sense. Focus on residues that you suspect might be important for the overall question you address. That said, pKa calculations are inherently difficult and can probably not be done reliably without lots of simulations. As such H++ probably come close to what we can currently accomplish within reasonable time for (nearly) static structures. Best, Erik 7 nov 2012 kl. 10.19 skrev Steven Neumann: Dear Gmx Users, I am trying to simulate protein-ligand interactions at specific pH=5. I processed my protein.pdb into the H++. As I see from th titration curve of the entire molecule it appears that at pH=5 the total charge should be equal to 2. When I process the obtained pdb from the server to pdb2gmx using -ignh I get the total charge of -3. Can anyone explain me this? In terms of small molecules how can I get parameters at specific pH? I am using Charmm and parachem.org does not support pH changes. Can anyone advise? thank you, Steven -- 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 --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- 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] What algorithm does g_sas use?
Hi Guang, Be careful with this tool. It's very fast and very good at what it's designed to do, but it does not appear to be designed to give accurate single-residue SASA (as you will read in the paper on the method employed). Definitely use g_sas for entire proteins or large cavities (it's blazing fast), but consider MSMS or DSSP for single-residue data. Matt Zwier On Wed, Nov 7, 2012 at 1:26 AM, jia jia jzg...@gmail.com wrote: Thanks! I've checked gromacs v 4.5.5 and got it. Seems all version before 4.0.5 doen't have that information.. Cheers Guang 2012/11/7, Justin Lemkul jalem...@vt.edu: On 11/7/12 1:18 AM, jia jia wrote: Dear gmx users: So sorry for bother you. Does any one know what algorithm g_sas use? There is no information about algorithm in help file, man page, and code. I think gromos use naccess method but not sure gromacs use the same one. References are printed in the screen output when running g_sas. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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/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 -- 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] Protein at given pH
On Wed, Nov 7, 2012 at 2:55 PM, Erik Marklund er...@xray.bmc.uu.se wrote: Hi, I've used the H++ server myself at times. My experience is that it's rather sensitive to the very fine detail of the input structure in some cases. I've had situations where H++ suggest one protonation state, then a short md simulation takes the system to a slightly different conformation that seem more prevalent but that yields another protonation state if sent to H++ again. Use all biochemical knowledge that you can muster to check that the output makes sense. Focus on residues that you suspect might be important for the overall question you address. That said, pKa calculations are inherently difficult and can probably not be done reliably without lots of simulations. As such H++ probably come close to what we can currently accomplish within reasonable time for (nearly) static structures. Best, Erik Thanks for this! Is it not better just to use pK values from the literature corresponding to given residue side chain? My protein is an alpha-helix. Thanks, Steven 7 nov 2012 kl. 10.19 skrev Steven Neumann: Dear Gmx Users, I am trying to simulate protein-ligand interactions at specific pH=5. I processed my protein.pdb into the H++. As I see from th titration curve of the entire molecule it appears that at pH=5 the total charge should be equal to 2. When I process the obtained pdb from the server to pdb2gmx using -ignh I get the total charge of -3. Can anyone explain me this? In terms of small molecules how can I get parameters at specific pH? I am using Charmm and parachem.org does not support pH changes. Can anyone advise? thank you, Steven -- 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 --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- 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] Protein at given pH
7 nov 2012 kl. 16.21 skrev Steven Neumann: On Wed, Nov 7, 2012 at 2:55 PM, Erik Marklund er...@xray.bmc.uu.se wrote: Hi, I've used the H++ server myself at times. My experience is that it's rather sensitive to the very fine detail of the input structure in some cases. I've had situations where H++ suggest one protonation state, then a short md simulation takes the system to a slightly different conformation that seem more prevalent but that yields another protonation state if sent to H++ again. Use all biochemical knowledge that you can muster to check that the output makes sense. Focus on residues that you suspect might be important for the overall question you address. That said, pKa calculations are inherently difficult and can probably not be done reliably without lots of simulations. As such H++ probably come close to what we can currently accomplish within reasonable time for (nearly) static structures. Best, Erik Thanks for this! Is it not better just to use pK values from the literature corresponding to given residue side chain? My protein is an alpha-helix. Thanks, Steven If such (reliable) data is available, then yes. Or it may serve as validation. Erik 7 nov 2012 kl. 10.19 skrev Steven Neumann: Dear Gmx Users, I am trying to simulate protein-ligand interactions at specific pH=5. I processed my protein.pdb into the H++. As I see from th titration curve of the entire molecule it appears that at pH=5 the total charge should be equal to 2. When I process the obtained pdb from the server to pdb2gmx using -ignh I get the total charge of -3. Can anyone explain me this? In terms of small molecules how can I get parameters at specific pH? I am using Charmm and parachem.org does not support pH changes. Can anyone advise? thank you, Steven -- 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 --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- 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 --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- 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] Double entries in block structure--problem with SHAKE
Dear All, As I am facing the following problem while using SHAKE to constrain some bonds, I have checked the mailing list but I think, this issue has not been resolved. So if anyone knows the solution kindly inform me. Program mdrun, VERSION 4.5.5 Source code file: invblock.c, line: 79 Fatal error: Double entries in block structure. Item 5247 is in blocks 1371 and 1370 Cannot make an unambiguous inverse block. Actually I need to fix some of the ligand bonds along with the covalent h-bonds (C-H, N-H, O-H etc.). What do you suggest to use for this multiple constraining problem ? Should I use SHAKE/LINCS for both type of bonds or anything else ? Thanks -- Tarak -- 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] Running Gromacs in Clusters
Hi, Sure you can go beyond 24 cores. I'm currently simulating ~170 000 atoms on 192 cores at ~45 ns a day. with half the number of processors I get ~27 ns a day. It will of course depend on the hardware, particular algorithms, run parameters, and on the system details. Erik 7 nov 2012 kl. 16.51 skrev Marcelo Depolo: Good afternoon, I wonder if anyone has experience running Gromacs in MPI. I'm paralleling the processes and want to know how many processors reduces the computation time to the minimum. I am currently using 24 processors for a system of 170 000 atoms and obtaining a simulation of 50ns in 15 days. There's a way to reduce more this computational time? Thanks in advance! -- Marcelo Depólo Polêto Departamento de Bioquímica e Biologia Molecular Universidade Federal de Viçosa - UFV *Website: http://opensourcebioinformatics.com/site/* -- 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 --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- 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] Temperature Histogram
Hello, I would like to calculate temperature in my system along the axis. Could you please tell me if there is a way to make a temperature histogram with Gromacs? Thank you for your attention. Cheers, Nino-- 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] Running Gromacs in Clusters
Hi Erik, That's good news! But i've got problems using more than one node per simulation (24 cores per node in my cluster). I don't know if it's a parallelization script problem or anything else. I'm using PBS scripts like this: *#!/bin/bash #PBS -N Gromacs #PBS -lselect=1:ncpus=24 #PBS -m ae #PBS -M marcelo@x date cd $PBS_O_WORKDIR source /usr/share/modules/init/bash source $HOME/gromacs module load mpi-lam7 HOSTLIST=`cat $PBS_NODEFILE |paste -s -d ,` cat $PBS_NODEFILE lamboot $PBS_NODEFILE mpirun -np 24 $HOME/bin/mdrun -e prt.edr -v -s prt.tpr -o prt.trr -c prt.gro -g date* I have tried to raise the number of nodes, of cores and both. I've got nothing. Do you have any suggestions? -- Marcelo Depólo Polêto Departamento de Bioquímica e Biologia Molecular Universidade Federal de Viçosa - UFV *Website: http://opensourcebioinformatics.com/site/* -- 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] Re: Self-diffusion in high temperature water
Sorry for the bump, but, please, does anybody know something of any study of the self-diffusion frequency spectrum of water done with GROMACS? I am not sure if it is something I am doing wrong, or if that is simple not possible to model with the program. Thanks, Ignacio On Tue, Oct 30, 2012 at 6:05 PM, Jose Ignacio Marquez nachomarq...@gmail.com wrote: Hi, I came across the following problem: when I calculate the frequency spectrum for high temperature (523 K) water, the results are inconsistent with the literature and analytical self-diffusion models. I am trying to reproduce the calculations by Martí, Guardia and Padro[1] of the vibrational spectrum of water along the liquid-vapor coexistence line. To do this, I first equilibrate the configuration for a given temperature and pressure for 10 o 20 ps with a short (0.1 fs) timestep, and then run the simulation for another 20 ps with the same timestep, dumping the velocity to the .trr file every few frames ([2] is the input file). Then, using g_velacc, I compute the VACF for H, O and the center of mass velocities. To compute the frequency spectrum I first compute the VACF for negative times as VACF(t) = VACF(t), and then calculate the FFT of the simmetrized VACF. I have done this for different flexible water models (SPC, SPC/E, TIP4P, TIP4P/2005) and all seem to reproduce the main features of the frequency spectrum, with slight variations. But, for some reason, the shape of the frequency spectra at low energies differs from what it should be expected for a diffusive regime. Instead of getting a Lorentzian shape, the limit of the spectrum for omega - 0 is a decreasing exponential. At first I thought this could have been caused by one particular water model, but actually I find the same behavior for all models, with different rho(omega=0) values, caused by different estimates of the diffusion coefficient. At ambient temperature (300 K), the Lorentzian shape is masked by the presence of intermolecular vibrations (Hydrogen bond bending and stretching), but at higher temperatures (523 K) diffusion dominate and the characteristic Lorentzian shape should be seen. To compare, I plotted[3] the spectrum of center of mass velocity computed at 523K with TIP5P/2005 Flex and the (scaled) spectrum of oxygen velocity, computed by Marti et al. I suspect the problem might be with tuning the options of GROMACS to ensure that the long time behavior is correctly represented, but I am fairly new to GROMACS and MD in general and I don't know how to achieve it. I tried running for longer times -up to 1 ns-, I tried running on double precision to ensure that is not a rounding problem, I tried to run on a larger system (to get a more converged statistical average), I modified g_velacc to save the VACF with more significant digits... but nothing seems to solve it. Any help on this will be appreciated. Thanks in advance, Ignacio [1] http://dx.doi.org/10.1063/1.471932http://link.aip.org/link/doi/10.1063/1.471932 [2] http://pastebin.com/z4bC5ZYZ [3] http://i.imgur.com/53R21.jpg -- 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] Temperature Histogram
On 11/7/12 11:42 AM, Samadashvili Nino wrote: Hello, I would like to calculate temperature in my system along the axis. Could you please tell me if there is a way to make a temperature histogram with Gromacs? Use g_energy to extract temperatures from the .edr file, then g_analyze -dist on that .xvg file. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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/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] Running Gromacs in Clusters
Hi, I looked at one of my old pbs jobs and noted that the following line works for me: #PBS -l nodes=X:ppn=Y where X is the number of nodes and ppn is the number of cores per node. Perhaps your batch system uses a different dialect. What errors do you get when you aim for more than one node? Furthermore, are you using virtual sites and constraints for your simulations? If not then you might be able to increase your simulation speed manifold. Erik 7 nov 2012 kl. 17.50 skrev Marcelo Depolo: Hi Erik, That's good news! But i've got problems using more than one node per simulation (24 cores per node in my cluster). I don't know if it's a parallelization script problem or anything else. I'm using PBS scripts like this: *#!/bin/bash #PBS -N Gromacs #PBS -lselect=1:ncpus=24 #PBS -m ae #PBS -M marcelo@x date cd $PBS_O_WORKDIR source /usr/share/modules/init/bash source $HOME/gromacs module load mpi-lam7 HOSTLIST=`cat $PBS_NODEFILE |paste -s -d ,` cat $PBS_NODEFILE lamboot $PBS_NODEFILE mpirun -np 24 $HOME/bin/mdrun -e prt.edr -v -s prt.tpr -o prt.trr -c prt.gro -g date* I have tried to raise the number of nodes, of cores and both. I've got nothing. Do you have any suggestions? -- Marcelo Depólo Polêto Departamento de Bioquímica e Biologia Molecular Universidade Federal de Viçosa - UFV *Website: http://opensourcebioinformatics.com/site/* -- 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 --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- 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] Double entries in block structure--problem with SHAKE
On 11/7/12 10:46 AM, tarak karmakar wrote: Dear All, As I am facing the following problem while using SHAKE to constrain some bonds, I have checked the mailing list but I think, this issue has not been resolved. So if anyone knows the solution kindly inform me. Program mdrun, VERSION 4.5.5 Source code file: invblock.c, line: 79 Fatal error: Double entries in block structure. Item 5247 is in blocks 1371 and 1370 Cannot make an unambiguous inverse block. Actually I need to fix some of the ligand bonds along with the covalent h-bonds (C-H, N-H, O-H etc.). What do you suggest to use for this multiple constraining problem ? Should I use SHAKE/LINCS for both type of bonds or anything else ? Can you explain in a bit greater depth what you're trying to do? Are you trying to constrain distances between atoms that are not covalently bonded? In that case, restraints are likely more appropriate than constraints, but we'll need more detail before anyone can give you any really productive suggestions. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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/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] Running Gromacs in Clusters
Hi, I usually go with openMPI. I think there are issues with LAM, but other probably know more about that. Erik 7 nov 2012 kl. 19.36 skrev Marcelo Depolo: Hi guys. I've tried your suggestions and had no sucess. I've got no resources available error but I checked out and 50% of the nodes are available. Perhaps, could be a library problem? Here, I compiled gromacs with MPI-LAM 7. Are you using another one? Thanks! -- Marcelo Depólo -- 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 --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- 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] What algorithm does g_sas use?
Thanks Matt! I've seen some vmd tcl scripts using msms to get the surface area. However I think as gromacs using united atom, I need too change radii parameters or in a more simple way, add all hydrogen back before calculation Cheers Guang 2012/11/8, Matthew Zwier mczw...@gmail.com: Hi Guang, Be careful with this tool. It's very fast and very good at what it's designed to do, but it does not appear to be designed to give accurate single-residue SASA (as you will read in the paper on the method employed). Definitely use g_sas for entire proteins or large cavities (it's blazing fast), but consider MSMS or DSSP for single-residue data. Matt Zwier On Wed, Nov 7, 2012 at 1:26 AM, jia jia jzg...@gmail.com wrote: Thanks! I've checked gromacs v 4.5.5 and got it. Seems all version before 4.0.5 doen't have that information.. Cheers Guang 2012/11/7, Justin Lemkul jalem...@vt.edu: On 11/7/12 1:18 AM, jia jia wrote: Dear gmx users: So sorry for bother you. Does any one know what algorithm g_sas use? There is no information about algorithm in help file, man page, and code. I think gromos use naccess method but not sure gromacs use the same one. References are printed in the screen output when running g_sas. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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/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 -- 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] Re: Running Gromacs in Clusters
I thought that at first, but other softwares run in parallel. If there's a problem, it' s somehow in the PBS. My guess is that my PBS don't allow the LAM library see others nodes. But I have no clue where the problem could be. I've tried eliminating the node=X and got the error. I've tried use node=2 (or any number higher than 1) and it goes to the queue even if there is empty nodes. I'm almost trying to compile gromacs again but now with OpemMPI... -- Marcelo Depólo -- 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
Fwd: [gmx-users] Re: Running Gromacs in Clusters
On Wed, Nov 7, 2012 at 11:24 PM, Marcelo Depolo marcelodep...@gmail.com wrote: I thought that at first, but other softwares run in parallel. If there's a problem, it' s somehow in the PBS. My guess is that my PBS don't allow the LAM library see others nodes. But I have no clue where the problem could be. I would be very surprised if this is true. The nornal sequences of events during submission process is the following: 1) The system looks into your submission script and finds out the resource requirements. 2) If the requirements are met, the job gets R status and the remaining commands (which do not start with #PBS) are executed. 3) If there is a problem with the message parallel interface or the [scientific] code, the job dies with some MPI-specific error message, or with code-specific message, or usually both of them. What I see in your report, your error message comes from PBS, i.e. neither MPI nor gromacs are launched. -- Dr. Vitaly V. Chaban MEMPHYS - Center for Biomembrane Physics Department of Physics, Chemistry and Pharmacy University of Southern Denmark Campusvej 55, 5230 Odense M, Denmark -- 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] Re: Running Gromacs in Clusters
On Wed, Nov 7, 2012 at 11:48 PM, Dr. Vitaly Chaban vvcha...@gmail.com wrote: On Wed, Nov 7, 2012 at 11:24 PM, Marcelo Depolo marcelodep...@gmail.com wrote: I thought that at first, but other softwares run in parallel. If there's a problem, it' s somehow in the PBS. My guess is that my PBS don't allow the LAM library see others nodes. But I have no clue where the problem could be. I would be very surprised if this is true. The nornal sequences of events during submission process is the following: 1) The system looks into your submission script and finds out the resource requirements. 2) If the requirements are met, the job gets R status and the remaining commands (which do not start with #PBS) are executed. 3) If there is a problem with the message parallel interface or the [scientific] code, the job dies with some MPI-specific error message, or with code-specific message, or usually both of them. What I see in your report, your error message comes from PBS, i.e. neither MPI nor gromacs are launched. Are you stating that other programs on your cluster run successfully on multiple nodes using the same (the #PBS part) submission script and only gromacs-jobs complain about lack of resources? I cannot believe... -- Dr. Vitaly V. Chaban MEMPHYS - Center for Biomembrane Physics Department of Physics, Chemistry and Pharmacy University of Southern Denmark Campusvej 55, 5230 Odense M, Denmark -- 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] Double entries in block structure--problem with SHAKE
Oh ! I'm sorry Justin Actually in my system I need to fix three types of bonds 1) Metal-Ligand distance at a particular value given in PDB ( not covalent) 2) I need to fix some of the bond lengths (covalent) for the substrate molecule. 3) Lastly the covalent H-bonds ( C-H, N-H, O-H etc.) My input .mdp file is given below ; 7.3.3 Run Control integrator = md-vv ; md integrator tinit = 0 ; [ps] starting time for run dt = 0.001 ; [ps] time step for integration nsteps = 500 ; maximum number of steps to integrate, 0.001 * 20,00,000 = 2 ns nstcomm = 1 ; [steps] frequency of mass motion removal comm_grps = Protein Non-Protein ; group(s) for center of mass motion removal ; 7.3.8 Output Control nstxout = 5000 ; [steps] freq to write coordinates to trajectory nstvout = 5000 ; [steps] freq to write velocities to trajectory nstfout = 5000 ; [steps] freq to write forces to trajectory nstlog = 1000 ; [steps] freq to write energies to log file nstenergy = 1000 ; [steps] freq to write energies to energy file nstxtcout = 1000 ; [steps] freq to write coordinates to xtc trajectory xtc_precision = 1000 ; [real] precision to write xtc trajectory xtc_grps= System; group(s) to write to xtc trajectory energygrps = System; group(s) to write to energy file ; 7.3.9 Neighbor Searching nstlist = 1 ; [steps] freq to update neighbor list ns_type = grid ; method of updating neighbor list pbc = xyz ; periodic boundary conditions in all directions rlist = 1.2 ; [nm] cut-off distance for the short-range neighbor list nsttcouple = 1 nstpcouple = 1 ; 7.3.10 Electrostatics coulombtype = PME ; Particle-Mesh Ewald electrostatics rcoulomb= 1.2 ; [nm] distance for Coulomb cut-off ; 7.3.11 VdW vdwtype = cut-off ; twin-range cut-off with rlist where rvdw = rlist rvdw= 1.2 ; [nm] distance for LJ cut-off DispCorr= EnerPres ; apply long range dispersion corrections for energy ; 7.3.13 Ewald fourierspacing = 0.12 ; [nm] grid spacing for FFT grid when using PME pme_order = 4 ; interpolation order for PME, 4 = cubic ewald_rtol = 1e-5 ; relative strength of Ewald-shifted potential at rcoulomb ; 7.3.14 Temperature Coupling tcoupl = Nose-Hoover ; Nose-Hoover temperature coupling tc_grps = ProteinNon-Protein; groups to couple seperately to temperature bath tau_t = 1.01.0; [ps] time constant for coupling ref_t = 300300; [K] reference temperature for coupling ; 7.3.15 Pressure Coupling pcoupl = MTTK ; pressure coupling where box vectors are variable pcoupltype = isotropic ; pressure coupling in x-y-z directions tau_p = 1.0 ; [ps] time constant for coupling compressibility = 4.5e-5; [bar^-1] compressibility ref_p = 1.0 ; [bar] reference pressure for coupling ; 7.3.17 Velocity Generation gen_vel = no; velocity generation turned off ; 7.3.18 Bonds constraints = h-bonds constraint_algorithm= SHAKE ; SHAKE Constraint Solver shake_tol = 1.0e-5 So I'm bit confused how to implement constraints algorithm for these type of problem. Thanks On Wed, Nov 7, 2012 at 11:54 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/7/12 10:46 AM, tarak karmakar wrote: Dear All, As I am facing the following problem while using SHAKE to constrain some bonds, I have checked the mailing list but I think, this issue has not been resolved. So if anyone knows the solution kindly inform me. Program mdrun, VERSION 4.5.5 Source code file: invblock.c, line: 79 Fatal error: Double entries in block structure. Item 5247 is in blocks 1371 and 1370 Cannot make an unambiguous inverse block. Actually I need to fix some of the ligand bonds along with the covalent h-bonds (C-H, N-H, O-H etc.). What do you suggest to use for this multiple constraining problem ?
[gmx-users] comparing gmx GB energy with Amber11
Hi,
I am comparing single point amber ff energies from gmx4.5.5 (double
precision) and Amber11.
All bonded and non-bonded energy terms are in very good agreement (within
0.1 kJ/mol) except GB:
gmx 'GB polarization' = -200 kJ/mol
amber 11 'EGB' = -283 kJ/mol.
I am basically trying to replicate Amber's igb=5 + large cutoff in gmx.
According to Amber manual igb=5 corresponds to model 2 of [2004 OBC
paper].
I translated this to the following mdp options:
implicit_solvent= GBSA
gb_algorithm= OBC
All cut-offs (rcoulomb, rvdw, rlist, rgbradii) larger than the size of the
molecule.
{gb_epsilon_solvent, gb_saltconc, gb_obc_alpha, gb_obc_beta, gb_obc_gamma,
gb_dielectric_offset} = corresponding Amber input.
Is that correct?
I realize that this is as much a question for Amber mailing list, but
trying here first! Any idea?
The molecule is ala-12. I'll be happy to send input files.
Thanks in advance
Sandeep
--
Postdoc
Wales Group
Cambridge
--
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