[gmx-users] implicit solvent simulation in gromacs
Hi All, I want to perform MD simulation of a protein in implicit solvent using gromacs 4.0.7. I looked into the manual but did not get any information regarding the implicit solvent. Is it avilable in gromacs? I searched in the mailing list and found someone in older mail said its not avilable. If it is avilable, could anybody please give me the mdp option. Is it okay to use 43a1 FF? Thanks Chanchal -- 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] implicit solvent simulation in gromacs
Chanchal wrote: Hi All, I want to perform MD simulation of a protein in implicit solvent using gromacs 4.0.7. I looked into the manual but did not get any information regarding the implicit solvent. Is it avilable in gromacs? I searched in the mailing list and found someone in older mail said its not avilable. If it is avilable, could anybody please give me the mdp option. Is it okay to use 43a1 FF? It is not available. Implicit solvent has been implemented in the development code and is expected in the next release. I think I posted the same thing just yesterday... -Justin Thanks Chanchal -- 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
Re: [gmx-users] implicit solvent simulation in gromacs
Implicit solvent are still not available in gromacs. Using 43a1 FF is fine, except with implicit solvent! Or you should have one compatible with it! On Apr 28, 2010, at 6:27 PM, Chanchal wrote: Hi All, I want to perform MD simulation of a protein in implicit solvent using gromacs 4.0.7. I looked into the manual but did not get any information regarding the implicit solvent. Is it avilable in gromacs? I searched in the mailing list and found someone in older mail said its not avilable. If it is avilable, could anybody please give me the mdp option. Is it okay to use 43a1 FF? Thanks Chanchal -- 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] Implicit solvent simulation
Hi Erik, Erik Lindahl wrote: Hi, On Jul 18, 2007, at 5:08 PM, David van der Spoel wrote: The version used by Alan Mark has never made it into gromacs. Rather, Erik Lindahl started the implementation of this stuff but did never finish it completely, due to other priorities I presume. We should however take out the variables to avoid confusion (unless someone provides a full implementation). Actually, technically the GB implementation is already in Gromacs (even assembly kernels), and quite correct, it's just that you don't have the born radii yet :-) I can't find any usage of the GB parameters as read from the mdp file - neither in the latest release nor the HEAD revision in the CVS. Is there another branch in the CVS you got that code in? I'm just curious as we worked on some GB models as well and using (at least the STILL) with assembly loops sounds very nice to me. Somewhat unrelated: I also saw the andersen_seed parameter and I was wondering if there is a code branch that contains an Andersen thermostat? Cheers, Edgar -- Edgar Luttmann, PhD Stanford University, Stanford, CA, USA Department of Chemistry, Group of Prof. Dr. V. Pande postdoctoral researcher: [EMAIL PROTECTED] - distributed computing Clark Center, 94305-5080 Stanford, CA, phone: (650) 723 1097 email: luttmann AT stanford.edu, www: http://www.stanford.edu/~luttmann ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Implicit solvent simulation
Although I realize it is the holiday season, at least in Europe, I would like to once more recommend the development wiki for documenting this kind of discussion, and for publishing specifications for algorithms, like (totally unrelated, but came up earlier today): http://wiki.gromacs.org/index.php/Cpp_replacement Heh - done for the surface stuff :-) Cheers, Erik ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Implicit solvent simulation
Hi, On Jul 19, 2007, at 10:15 AM, Edgar Luttmann wrote: I can't find any usage of the GB parameters as read from the mdp file - neither in the latest release nor the HEAD revision in the CVS. Is there another branch in the CVS you got that code in? No, at least not publicly available atm. And even in our own hacks we don't use any the mdp parameters yet since we (i) only support Still, (ii) calculate the radii every step, and (iii) haven't bothered with salts yet :-) Cheers, Erik ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Implicit solvent simulation
Thank you for your kind reply, Stephane. Anyhow it is a little disappointing that Generalized-Born is not implemented in Gromacs. Sincerely, Seungpyo Hong On 7/16/07, Stéphane Téletchéa [EMAIL PROTECTED] wrote: SeungPyo Hong a écrit : Dear gmx-users, Recently I want to perform MD for protein with implicit solvent model. Gromacs does not seem to support it. Could you let me know where to find information about implicit solvent simulation with Gromacs? Also I will be glad if you tell me your opinion about the implicit solvent simulation to protein. Thank you. There is no Generalised-Born approach implemented (at least available) but you may consider reaction field. See chapter 7, paragraph Electrostatics and VdW. Cheers, Stéphane -- Stéphane Téletchéa, PhD. http://www.steletch.org Unité Mathématique Informatique et Génome http://migale.jouy.inra.fr/mig INRA, Domaine de Vilvert Tél : (33) 134 652 891 78352 Jouy-en-Josas cedex, France Fax : (33) 134 652 901 ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Implicit solvent simulation
SeungPyo Hong wrote: Thank you for your kind reply, Stephane. Anyhow it is a little disappointing that Generalized-Born is not implemented in Gromacs. I've put it on the development TODO list (feel free to volunteer) http://wiki.gromacs.org/index.php/Implicit_Solvent The reason it is not there is because none of the developers has considered it worthwhile. -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Implicit solvent simulation
Hi, Just to let people know in case they are unaware there is a paper where implicit solvent models have been implemented in GROMACS, the paper can be found using the following link: http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmedpubmedid=15814616 Tom --On Wednesday, July 18, 2007 15:39:43 +0200 David van der Spoel [EMAIL PROTECTED] wrote: SeungPyo Hong wrote: Thank you for your kind reply, Stephane. Anyhow it is a little disappointing that Generalized-Born is not implemented in Gromacs. I've put it on the development TODO list (feel free to volunteer) http://wiki.gromacs.org/index.php/Implicit_Solvent The reason it is not there is because none of the developers has considered it worthwhile. -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- TJ Piggot [EMAIL PROTECTED] University of Bristol, UK. ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Implicit solvent simulation
Dear Tom, The paper is available and was mentioned in the list. The model, however, isn't available AFAIK. Ran. TJ Piggot wrote: Hi, Just to let people know in case they are unaware there is a paper where implicit solvent models have been implemented in GROMACS, the paper can be found using the following link: http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmedpubmedid=15814616 Tom --On Wednesday, July 18, 2007 15:39:43 +0200 David van der Spoel [EMAIL PROTECTED] wrote: SeungPyo Hong wrote: Thank you for your kind reply, Stephane. Anyhow it is a little disappointing that Generalized-Born is not implemented in Gromacs. I've put it on the development TODO list (feel free to volunteer) http://wiki.gromacs.org/index.php/Implicit_Solvent The reason it is not there is because none of the developers has considered it worthwhile. -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone:+46184714205. Fax: +4618511755. [EMAIL PROTECTED][EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- TJ Piggot [EMAIL PROTECTED] University of Bristol, UK. ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- -- Ran Friedman Postdoctoral Fellow Computational Structural Biology Group (A. Caflisch) Department of Biochemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich, Switzerland Tel. +41-44-6355593 Email: [EMAIL PROTECTED] Skype: ran.friedman -- ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Implicit solvent simulation
If you REALLY want implicit solvent then i suggest you contact the authors and ask them about it, however i (like most others i think) have never needed to use implicit solvent. Tom --On Wednesday, July 18, 2007 16:17:01 +0200 Ran Friedman [EMAIL PROTECTED] wrote: Dear Tom, The paper is available and was mentioned in the list. The model, however, isn't available AFAIK. Ran. TJ Piggot wrote: Hi, Just to let people know in case they are unaware there is a paper where implicit solvent models have been implemented in GROMACS, the paper can be found using the following link: http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmedpubmedid =15814616 Tom --On Wednesday, July 18, 2007 15:39:43 +0200 David van der Spoel [EMAIL PROTECTED] wrote: SeungPyo Hong wrote: Thank you for your kind reply, Stephane. Anyhow it is a little disappointing that Generalized-Born is not implemented in Gromacs. I've put it on the development TODO list (feel free to volunteer) http://wiki.gromacs.org/index.php/Implicit_Solvent The reason it is not there is because none of the developers has considered it worthwhile. -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone:+46184714205. Fax: +4618511755. [EMAIL PROTECTED][EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- TJ Piggot [EMAIL PROTECTED] University of Bristol, UK. ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- -- Ran Friedman Postdoctoral Fellow Computational Structural Biology Group (A. Caflisch) Department of Biochemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich, Switzerland Tel. +41-44-6355593 Email: [EMAIL PROTECTED] Skype: ran.friedman -- ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- TJ Piggot [EMAIL PROTECTED] University of Bristol, UK. ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Implicit solvent simulation
I asked for and received the code a couple of years ago. As the paper indicates, it's in an ancient version of GROMACS...which creates challenges. Also, the different models (Still, etc.) are implemented in independent versions of the code. Also, the GB part is actually implemented in FORTRAN. Jonathan Jonathan Moore, Ph.D. Research and Engineering Sciences - New Products Core RD The Dow Chemical Company 1702 Building, Office 300E Midland, MI 48674 USA Phone: (989) 636-9765 Fax: (989) 636-4019 E Mail: [EMAIL PROTECTED] -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Ran Friedman Sent: Wednesday, July 18, 2007 10:17 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Implicit solvent simulation Dear Tom, The paper is available and was mentioned in the list. The model, however, isn't available AFAIK. Ran. TJ Piggot wrote: Hi, Just to let people know in case they are unaware there is a paper where implicit solvent models have been implemented in GROMACS, the paper can be found using the following link: http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmedpubmedid =15814616 Tom --On Wednesday, July 18, 2007 15:39:43 +0200 David van der Spoel [EMAIL PROTECTED] wrote: SeungPyo Hong wrote: Thank you for your kind reply, Stephane. Anyhow it is a little disappointing that Generalized-Born is not implemented in Gromacs. I've put it on the development TODO list (feel free to volunteer) http://wiki.gromacs.org/index.php/Implicit_Solvent The reason it is not there is because none of the developers has considered it worthwhile. -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone:+46184714205. Fax: +4618511755. [EMAIL PROTECTED][EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- TJ Piggot [EMAIL PROTECTED] University of Bristol, UK. ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- -- Ran Friedman Postdoctoral Fellow Computational Structural Biology Group (A. Caflisch) Department of Biochemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich, Switzerland Tel. +41-44-6355593 Email: [EMAIL PROTECTED] Skype: ran.friedman -- ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Implicit solvent simulation
Moore, Jonathan (J) a écrit : I asked for and received the code a couple of years ago. As the paper indicates, it's in an ancient version of GROMACS...which creates challenges. Also, the different models (Still, etc.) are implemented in independent versions of the code. Also, the GB part is actually implemented in FORTRAN. Jonathan You are lucky, i did so and never got the code. This raises the question about GPL violations and publication trustworthy, since it is published, can we consider the code has been made publicly available since provided once a paper has been published, we are supposed to be able to reproduce the published work. I had not pushed a lot for getting the code but since traces are 'still' in gromacs code (in every mdp-generated file at least, there is a mention about GB parameters), it would be nice to have an official statement on this from the core developpers of GROMACS. I'm not trying to get any grief here, if you consider this a non-issue, please ignore the message, that'll be enough to me. Cheers, Stéphane -- Stéphane Téletchéa, PhD. http://www.steletch.org Unité Mathématique Informatique et Génome http://migale.jouy.inra.fr/mig INRA, Domaine de Vilvert Tél : (33) 134 652 891 78352 Jouy-en-Josas cedex, France Fax : (33) 134 652 901 ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Implicit solvent simulation
Stéphane Téletchéa wrote: Moore, Jonathan (J) a écrit : I asked for and received the code a couple of years ago. As the paper indicates, it's in an ancient version of GROMACS...which creates challenges. Also, the different models (Still, etc.) are implemented in independent versions of the code. Also, the GB part is actually implemented in FORTRAN. Jonathan You are lucky, i did so and never got the code. This raises the question about GPL violations and publication trustworthy, since it is published, can we consider the code has been made publicly available since provided once a paper has been published, we are supposed to be able to reproduce the published work. I had not pushed a lot for getting the code but since traces are 'still' in gromacs code (in every mdp-generated file at least, there is a mention about GB parameters), it would be nice to have an official statement on this from the core developpers of GROMACS. I'm not trying to get any grief here, if you consider this a non-issue, please ignore the message, that'll be enough to me. Cheers, Stéphane The version used by Alan Mark has never made it into gromacs. Rather, Erik Lindahl started the implementation of this stuff but did never finish it completely, due to other priorities I presume. We should however take out the variables to avoid confusion (unless someone provides a full implementation). -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Implicit solvent simulation
Hi, On Jul 18, 2007, at 5:08 PM, David van der Spoel wrote: The version used by Alan Mark has never made it into gromacs. Rather, Erik Lindahl started the implementation of this stuff but did never finish it completely, due to other priorities I presume. We should however take out the variables to avoid confusion (unless someone provides a full implementation). Actually, technically the GB implementation is already in Gromacs (even assembly kernels), and quite correct, it's just that you don't have the born radii yet :-) The last couple of years we've mainly done membrane stuff where it's not useful for my students, and thus not a priority to implement. However, recently Per Larsson has finished C implementations of the Still radius calculations that I've started optimizing. The big remaining task is the SA part of GB/SA, i.e. the surface calculation, which also needs to be optimized and preferrably parallelized (harder) to be useful. Fan Hao actually offered us the code he wrote with Alan, but the challengefor us isn't to write a trivial Still GB implementation, but to make it perform well. There's little point in having a GB implementation that is slower than the fast explicit-solvent simulations in Gromacs! Cheers, Erik ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Implicit solvent simulation
Selon Erik Lindahl [EMAIL PROTECTED]: Hi, On Jul 18, 2007, at 5:08 PM, David van der Spoel wrote: The version used by Alan Mark has never made it into gromacs. Rather, Erik Lindahl started the implementation of this stuff but did never finish it completely, due to other priorities I presume. We should however take out the variables to avoid confusion (unless someone provides a full implementation). Actually, technically the GB implementation is already in Gromacs (even assembly kernels), and quite correct, it's just that you don't have the born radii yet :-) The last couple of years we've mainly done membrane stuff where it's not useful for my students, and thus not a priority to implement. However, recently Per Larsson has finished C implementations of the Still radius calculations that I've started optimizing. The big remaining task is the SA part of GB/SA, i.e. the surface calculation, which also needs to be optimized and preferrably parallelized (harder) to be useful. Fan Hao actually offered us the code he wrote with Alan, but the challengefor us isn't to write a trivial Still GB implementation, but to make it perform well. There's little point in having a GB implementation that is slower than the fast explicit-solvent simulations in Gromacs! Happy to hear that, if you need some beta-tester for validation and performance tests, i'm your man :-) Cheers, Stéphane Téletchéa ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Implicit solvent simulation
[EMAIL PROTECTED] wrote: Selon Erik Lindahl [EMAIL PROTECTED]: Hi, On Jul 18, 2007, at 5:08 PM, David van der Spoel wrote: The version used by Alan Mark has never made it into gromacs. Rather, Erik Lindahl started the implementation of this stuff but did never finish it completely, due to other priorities I presume. We should however take out the variables to avoid confusion (unless someone provides a full implementation). Actually, technically the GB implementation is already in Gromacs (even assembly kernels), and quite correct, it's just that you don't have the born radii yet :-) The last couple of years we've mainly done membrane stuff where it's not useful for my students, and thus not a priority to implement. However, recently Per Larsson has finished C implementations of the Still radius calculations that I've started optimizing. The big remaining task is the SA part of GB/SA, i.e. the surface calculation, which also needs to be optimized and preferrably parallelized (harder) to be useful. Erik, didn't you say once that you implemented fast area calculations and derivatives? It's an interesting CS problem, but there certainly are at least a couple of papers on these topics. Fan Hao actually offered us the code he wrote with Alan, but the challengefor us isn't to write a trivial Still GB implementation, but to make it perform well. There's little point in having a GB implementation that is slower than the fast explicit-solvent simulations in Gromacs! Happy to hear that, if you need some beta-tester for validation and performance tests, i'm your man :-) You can help already now, by heading over to http://wiki.gromacs.org/index.php/Implicit_Solvent and adding more documentation. Although I realize it is the holiday season, at least in Europe, I would like to once more recommend the development wiki for documenting this kind of discussion, and for publishing specifications for algorithms, like (totally unrelated, but came up earlier today): http://wiki.gromacs.org/index.php/Cpp_replacement Cheers, -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Implicit solvent simulation
There is a niche for implicit solvent if you need to do more extensive conformational sampling than you can achieve with atomically detailed solvent---and if you can plausibly argue that you are not introducing such egregious systematic errors that you are just sampling more junk. At 09:23 AM 7/18/2007, TJ Piggot wrote: If you REALLY want implicit solvent then i suggest you contact the authors and ask them about it, however i (like most others i think) have never needed to use implicit solvent. Tom --On Wednesday, July 18, 2007 16:17:01 +0200 Ran Friedman [EMAIL PROTECTED] wrote: Dear Tom, The paper is available and was mentioned in the list. The model, however, isn't available AFAIK. Ran. TJ Piggot wrote: Hi, Just to let people know in case they are unaware there is a paper where implicit solvent models have been implemented in GROMACS, the paper can be found using the following link: http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmedpubmedid =15814616 Tom --On Wednesday, July 18, 2007 15:39:43 +0200 David van der Spoel [EMAIL PROTECTED] wrote: SeungPyo Hong wrote: Thank you for your kind reply, Stephane. Anyhow it is a little disappointing that Generalized-Born is not implemented in Gromacs. I've put it on the development TODO list (feel free to volunteer) http://wiki.gromacs.org/index.php/Implicit_Solvent The reason it is not there is because none of the developers has considered it worthwhile. -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone:+46184714205. Fax: +4618511755. [EMAIL PROTECTED][EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- TJ Piggot [EMAIL PROTECTED] University of Bristol, UK. ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- -- Ran Friedman Postdoctoral Fellow Computational Structural Biology Group (A. Caflisch) Department of Biochemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich, Switzerland Tel. +41-44-6355593 Email: [EMAIL PROTECTED] Skype: ran.friedman -- ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- TJ Piggot [EMAIL PROTECTED] University of Bristol, UK. ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php - Eric Jakobsson, Ph.D. Professor, Department of Molecular and Integrative Physiology, and of Biochemistry, and of the Center for Biophysics and Computational Biology Senior Research Scientist, National Center for Supercomputing Applications Professor, Beckman Institute for Advanced Science and Technology 3261 Beckman Institute, mc251 University of Illinois, Urbana, IL 61801 ph. 217-244-2896 Fax 217 244 9757 ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Implicit solvent simulation
Dear gmx-users, Recently I want to perform MD for protein with implicit solvent model. Gromacs does not seem to support it. Could you let me know where to find information about implicit solvent simulation with Gromacs? Also I will be glad if you tell me your opinion about the implicit solvent simulation to protein. Thank you. ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Implicit solvent simulation
SeungPyo Hong a écrit : Dear gmx-users, Recently I want to perform MD for protein with implicit solvent model. Gromacs does not seem to support it. Could you let me know where to find information about implicit solvent simulation with Gromacs? Also I will be glad if you tell me your opinion about the implicit solvent simulation to protein. Thank you. There is no Generalised-Born approach implemented (at least available) but you may consider reaction field. See chapter 7, paragraph Electrostatics and VdW. Cheers, Stéphane -- Stéphane Téletchéa, PhD. http://www.steletch.org Unité Mathématique Informatique et Génome http://migale.jouy.inra.fr/mig INRA, Domaine de Vilvert Tél : (33) 134 652 891 78352 Jouy-en-Josas cedex, France Fax : (33) 134 652 901 ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
