Re: [gmx-users] Missing terminal cap group
Dear Justin, Thanks for the reply. I just had a recheck of Gromacs Charmm36ff provided in Grocmacs website ( http://www.gromacs.org/Downloads/User_contributions/Force_fields). Unfortunately ACE group is missing in the .rtp file and also, in the .n.tdb file. But, it is present in the Chramm27ff, which came with Gromacs package itself. The Charmm36ff provided by http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs also have the ACE group in the .rtp file. Is it okay if I replace the charmm36ff in gromacs/share/gromacs/top/ folder ( downloaded from http://www.gromacs.org/Downloads/User_contributions/Force_fields ) with the one from MacKerell lab? Many thanks Aneesh On Fri, Jul 3, 2015 at 4:46 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/3/15 11:10 AM, anu chandra wrote: Dear Gromacs users, I am trying to generate topology for a membrane protein, which is capped with acetyl and methyl amide group, using Charmm36 force field in Gromacs. Unfortunately, the acetyl (ACE) group is seems to be missing in the Gromacs Charmm36 force field. Can anybody suggest me a way to add acetyl group with Charmm36 force field? The ACE capping group is present in the force field .rtp, so it's not missing. If it's not in your coordinate file, then you need to build it with some external software. The GROMACS website has some suggestions for that. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Topology for ready-made membrane protein system
Dear Justin, Do I need to add lipid topology manually, if I use Charmm36 force filed that have protein and lipid parameters together? Thanks Anu On Fri, Jul 3, 2015 at 4:47 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/3/15 7:56 AM, anu chandra wrote: Dear Gromacs users, I am working with membrane proteins. I have generated the membrane-protein system ( contains lipids, protein, water and ions) with some specification. For eg., I have positioned few ions and water molecules at particular location using some in-house programs. Now, I would like to generate topology for the my system in order to run MD using Gromacs. Since my system is ready-made, I cant follow the methodology adopt by Gromcas membrane-protein tutorials. Hence, can anybody suggest me a way to generate Gromacs inputs files for such ready-made membrane-protein systems? Process the protein with pdb2gmx and add an #include statements for the lipid topology. Then modify [molecules] to account for what's actually in the system. Water and ion topologies will automatically be #included in the .top written by pdb2gmx. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Installation problem
Hi, I want to install gromacs 5.0.5 but after issuing this command: cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON I encounter the folloeing error: Downloading: http://gerrit.gromacs.org/download/regressiontests-5.0.5.tar.gz CMake Error at tests/CMakeLists.txt:57 (message): error: downloading 'http://gerrit.gromacs.org/download/regressiontests-5.0.5.tar.gz' failed status_code: 1 status_string: unsupported protocol log: About to connect() to gerrit.gromacs.org port 80 (#0) Trying 130.237.25.133... connected Connected to gerrit.gromacs.org (130.237.25.133) port 80 (#0) GET /download/regressiontests-5.0.5.tar.gz HTTP/1.1 Host: gerrit.gromacs.org Accept: */* HTTP/1.1 302 Found Date: Mon, 06 Jul 2015 09:29:46 GMT Server: Apache/2.2.22 (Ubuntu) Location: https://kth.box.com/shared/static/ft4o4qpm318vsrori35sqhcuv5w6qjnu.gz Vary: Accept-Encoding Content-Length: 337 Content-Type: text/html; charset=iso-8859-1 Ignoring the response-body !DOCTYPE HTML PUBLIC -//IETF//DTD HTML 2.0//EN htmlhead title302 Found/title /headbody h1Found/h1 pThe document has moved a href= https://kth.box.com/shared/static/ft4o4qpm318vsrori35sqhcuv5w6qjnu.gz; https://kth.box.com/shared/static/ft4o4qpm318vsrori35sqhcuv5w6qjnu.gz here/a./p hr addressApache/2.2.22 (Ubuntu) Server at gerrit.gromacs.org Port 80/address /body/html Connection #0 to host gerrit.gromacs.org left intact Issue another request to this URL: 'https://kth.box.com/shared/static/ft4o4qpm318vsrori35sqhcuv5w6qjnu.gz' libcurl was built with SSL disabled, https: not supported! unsupported protocol Closing connection #0 - what can I do? does installing another version of Cmake makes any difference ? Best Regards, Nima Soltani -- Graduate Student of Physical Chemistry Department of Chemistry, Sharif University of Technology. = -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Installation problem
Hi, The real problem description is at the end. You are doing the download with a cmake that relies on curl that relies on libssl and that doesn't support the boring standard https protocol. Perhaps your operating system is too old to be useful. You can bypass this and get the tests yourself, following http://www.gromacs.org/Documentation/Installation_Instructions_5.0#testing-gromacs-for-correctness Mark On Mon, 6 Jul 2015 12:31 Nima Soltani nima@gmail.com wrote: Hi, I want to install gromacs 5.0.5 but after issuing this command: cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON I encounter the folloeing error: Downloading: http://gerrit.gromacs.org/download/regressiontests-5.0.5.tar.gz CMake Error at tests/CMakeLists.txt:57 (message): error: downloading 'http://gerrit.gromacs.org/download/regressiontests-5.0.5.tar.gz' failed status_code: 1 status_string: unsupported protocol log: About to connect() to gerrit.gromacs.org port 80 (#0) Trying 130.237.25.133... connected Connected to gerrit.gromacs.org (130.237.25.133) port 80 (#0) GET /download/regressiontests-5.0.5.tar.gz HTTP/1.1 Host: gerrit.gromacs.org Accept: */* HTTP/1.1 302 Found Date: Mon, 06 Jul 2015 09:29:46 GMT Server: Apache/2.2.22 (Ubuntu) Location: https://kth.box.com/shared/static/ft4o4qpm318vsrori35sqhcuv5w6qjnu.gz Vary: Accept-Encoding Content-Length: 337 Content-Type: text/html; charset=iso-8859-1 Ignoring the response-body !DOCTYPE HTML PUBLIC -//IETF//DTD HTML 2.0//EN htmlhead title302 Found/title /headbody h1Found/h1 pThe document has moved a href= https://kth.box.com/shared/static/ft4o4qpm318vsrori35sqhcuv5w6qjnu.gz; https://kth.box.com/shared/static/ft4o4qpm318vsrori35sqhcuv5w6qjnu.gz here/a./p hr addressApache/2.2.22 (Ubuntu) Server at gerrit.gromacs.org Port 80/address /body/html Connection #0 to host gerrit.gromacs.org left intact Issue another request to this URL: 'https://kth.box.com/shared/static/ft4o4qpm318vsrori35sqhcuv5w6qjnu.gz' libcurl was built with SSL disabled, https: not supported! unsupported protocol Closing connection #0 - what can I do? does installing another version of Cmake makes any difference ? Best Regards, Nima Soltani -- Graduate Student of Physical Chemistry Department of Chemistry, Sharif University of Technology. = -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Topology for ready-made membrane protein system
On 7/6/15 7:05 AM, anu chandra wrote: Dear Justin, Do I need to add lipid topology manually, if I use Charmm36 force filed that have protein and lipid parameters together? You always need a topology for any molecule in the system. -Justin Thanks Anu On Fri, Jul 3, 2015 at 4:47 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/3/15 7:56 AM, anu chandra wrote: Dear Gromacs users, I am working with membrane proteins. I have generated the membrane-protein system ( contains lipids, protein, water and ions) with some specification. For eg., I have positioned few ions and water molecules at particular location using some in-house programs. Now, I would like to generate topology for the my system in order to run MD using Gromacs. Since my system is ready-made, I cant follow the methodology adopt by Gromcas membrane-protein tutorials. Hence, can anybody suggest me a way to generate Gromacs inputs files for such ready-made membrane-protein systems? Process the protein with pdb2gmx and add an #include statements for the lipid topology. Then modify [molecules] to account for what's actually in the system. Water and ion topologies will automatically be #included in the .top written by pdb2gmx. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Topology for ready-made membrane protein system
Hi, You need a topology for each moleculetype, and parameters for the interactions they require. These are separate issues. Mark On Mon, 6 Jul 2015 13:05 anu chandra anu80...@gmail.com wrote: Dear Justin, Do I need to add lipid topology manually, if I use Charmm36 force filed that have protein and lipid parameters together? Thanks Anu On Fri, Jul 3, 2015 at 4:47 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/3/15 7:56 AM, anu chandra wrote: Dear Gromacs users, I am working with membrane proteins. I have generated the membrane-protein system ( contains lipids, protein, water and ions) with some specification. For eg., I have positioned few ions and water molecules at particular location using some in-house programs. Now, I would like to generate topology for the my system in order to run MD using Gromacs. Since my system is ready-made, I cant follow the methodology adopt by Gromcas membrane-protein tutorials. Hence, can anybody suggest me a way to generate Gromacs inputs files for such ready-made membrane-protein systems? Process the protein with pdb2gmx and add an #include statements for the lipid topology. Then modify [molecules] to account for what's actually in the system. Water and ion topologies will automatically be #included in the .top written by pdb2gmx. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] GPU/CPU load imbalance
I have 3x GTX 970 for 1x Intel i7-5820K with X99-E WS motherboard to remove PCIe limitations. So I have 4 threads/gpu and I face load imbalances. I am wondering if it will be a good idea to use reaction-field instead of PME in order to reduce the processor load (It would be less accurate). Let me know if you have any suggestions for proper load balancing. Thank you. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Missing terminal cap group
On 7/6/15 6:59 AM, anu chandra wrote: Dear Justin, Thanks for the reply. I just had a recheck of Gromacs Charmm36ff provided in Grocmacs website ( http://www.gromacs.org/Downloads/User_contributions/Force_fields). Unfortunately ACE group is missing in the .rtp file and also, in the .n.tdb file. But, it is present in the Chramm27ff, which came with Gromacs package itself. The Charmm36ff provided by http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs also have the ACE group in the .rtp file. Is it okay if I replace the charmm36ff in gromacs/share/gromacs/top/ folder ( downloaded from http://www.gromacs.org/Downloads/User_contributions/Force_fields ) with the one from MacKerell lab? Use the whole force field from our lab; don't piece together files from different places. The tarball on the Downloads site (as the description says) is not actually CHARMM36; it is a hybrid of CHARMM22/CMAP for proteins and CHARMM36 for lipids. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Gromcas tools listing with 'gmx'
Dear Gromcas users, I have installed latest version of Gromcas and while using I am adding 'gmx' prior the all the Gromacs tools ( for eg, pdb2gmx). Unfortunately, the 'TAB' key failed to list the possible commands if I use 'gmx' prior to any Gromacs tools.This leaves me each time to remember the exact tool name before using it. Is this normal with using gmx or am I missed something while installation? Many thanks Anu -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] GROMACS 5.1 release candidate available
Hi GROMACS users, The first release candidate of GROMACS 5.1 is now available! We are making this available to you to get a near-final taste of how GROMACS 5.1 will look and work, and most importantly to get feedback from you about how well things work. While we try our hardest to keep the quality of GROMACS as high as possible, we’re human, we overlook things while doing other things, and we need your many pairs of eyes to help build a tool that we can all use to do good science! We really need you to test your kinds of simulation on your hardware, both for correctness and performance. This is particularly important if you are using older hardware or compilers, because we don’t test much on them. Please do not use this version for doing science you plan to publish - it needs more testing before it’s reliable enough for that. Similarly, please don’t use this version as a base for a project that bundles or forks GROMACS. What new things can you expect? (See the release notes for details) * OpenCL support, thanks to the good folks at StreamComputing * ever more advanced CUDA support, thanks to help from Nvidia * improved multi-level heterogenous load balancing and default choices * intermolecular bonded interactions (useful for ligand-binding calculations) * no more symlinks from grompp to gmx grompp, etc. (as forecast in GROMACS 5) * new unified documentation, including new User Guide (see below) * several improved analysis tools * some minor improvements to simulation performance * enhancements to the pull code Still in the pipeline * more documentation The new documentation is aimed at bringing together all of our documentation together with the source code, and making it easier to update alongside the code, be in a common reStructuredText format, and deploy as a coherent webpage that can match a single code version. There's definitely rough edges, and we still need to bring more content in from the wiki. Any help would be most welcome here. Which bits do you find most useful, or in need of improvement? What’s hard to understand about the new organization? How can we improve it? Just so you know, a fair bit of the work done since 5.0 has been re-organizational, rather than new features or faster performance. The payoff is yet to come... There’s lots of other new things, and old things removed - please see the link to the release notes. All the content of GROMACS 5.0.5 (plus several yet-to-be-released bug fixes) is present, apart from features that have been removed. If all goes to plan, we hope to ship the final 5.1 release in the next few weeks, but that relies on people joining in and helping us test! We hope you will consider making that contribution, so that we can continue to deliver high-quality free simulation software that will be useful to you on day 1. You can find the code, manual, release notes, installation instructions and test suite at the links below. Code: see http://www.gromacs.org/Downloads Documentation: http://manual.gromacs.org/documentation/5.1-rc1/index.html (includes install guide, user guide, reference manual) Release Notes: http://manual.gromacs.org/documentation/5.1-rc1/ReleaseNotes/index.html Test Suite: http://gerrit.gromacs.org/download/regressiontests-5.1-rc1.tar.gz Happy testing! Mark Abraham GROMACS development manager -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Gromcas tools listing with 'gmx'
This is to confirm that I also get an embarrassment of choices on my local box, but empty on the cluster nodes. Otherwise, everything works the same way on both. Not that I care about the listing, but yeah. :) Alex On Mon, Jul 6, 2015 at 1:14 PM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, Having sourced GMXRC in my bash shell, typing gmx, space, TAB gives me an embarassment of choices. Does it not for you? Mark On Mon, Jul 6, 2015 at 5:36 PM anu chandra anu80...@gmail.com wrote: Dear Gromcas users, I have installed latest version of Gromcas and while using I am adding 'gmx' prior the all the Gromacs tools ( for eg, pdb2gmx). Unfortunately, the 'TAB' key failed to list the possible commands if I use 'gmx' prior to any Gromacs tools.This leaves me each time to remember the exact tool name before using it. Is this normal with using gmx or am I missed something while installation? Many thanks Anu -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] GPU gromacs
Of course you can, but with such a low-end mobile GPU you may not even gain performance from offloading computation from the CPU and additionally you may have issues with cooling too. You can simply try comparing performance with -nb cpu and -nb gpu to see if using the GPU improves performance at all. -- Szilárd On Sat, Jul 4, 2015 at 1:40 PM, James Lord jjamesgreen...@gmail.com wrote: Hi All, I have a system with 300k atoms, I don't have access to HPC facilities, Is it possible to run gromcas on GPU on a desktop with following graphic card for up to 200-300 ns? 00:02.0 VGA compatible controller: Intel Corporation 3rd Gen Core processor Graphics Controller (rev 09) 01:00.0 VGA compatible controller: NVIDIA Corporation GF108M [GeForce GT 635M] (rev a1) any thoughts is greatly appreciated. Cheers James -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] GPU/CPU load imbalance
What kind of load imbalance? I assume you are referring to CPU-GPU imbalance as your runs are CPU-bound. In that case the only thing that helps is either porting code to CUDA or a faster CPU. Reaction field electrostatics will help too in getting better performance in CPU-bound runs, but beware that you'll have to justify the choice of deviating form the most established way of treating electrostatics! -- Szilárd On Mon, Jul 6, 2015 at 1:32 PM, Pappu Kumar papu...@yahoo.com wrote: I have 3x GTX 970 for 1x Intel i7-5820K with X99-E WS motherboard to remove PCIe limitations. So I have 4 threads/gpu and I face load imbalances. I am wondering if it will be a good idea to use reaction-field instead of PME in order to reduce the processor load (It would be less accurate). Let me know if you have any suggestions for proper load balancing. Thank you. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Gromcas tools listing with 'gmx'
Hi, Having sourced GMXRC in my bash shell, typing gmx, space, TAB gives me an embarassment of choices. Does it not for you? Mark On Mon, Jul 6, 2015 at 5:36 PM anu chandra anu80...@gmail.com wrote: Dear Gromcas users, I have installed latest version of Gromcas and while using I am adding 'gmx' prior the all the Gromacs tools ( for eg, pdb2gmx). Unfortunately, the 'TAB' key failed to list the possible commands if I use 'gmx' prior to any Gromacs tools.This leaves me each time to remember the exact tool name before using it. Is this normal with using gmx or am I missed something while installation? Many thanks Anu -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] g_clustsize
On 06/07/15 06:05, V.V.Chaban wrote: The sum of these probabilities is never the same. It is confusing. If no clusters exist (all particles are lone) then the sum of probabilities equals the sum of all particles. If clusters exist, the sum is different and it is unclear how it is derived. If the output property is still a probability: is it a probability that N atoms exist as a cluster or it is a probability that such a cluster exists within all possible clusters (a fraction of a given cluster)? You have to integrate y*x I would say to normalize it. On Sun, Jul 5, 2015 at 5:40 PM, David van der Spoel sp...@xray.bmc.uu.se wrote: On 05/07/15 14:09, V.V.Chaban wrote: g_clustsize creates file 'histo-clust.xvg'. What does y-axis in this file mean? If this is a probability than of what? Probability of cluster size, what else? @title Cluster size distribution @xaxis label Cluster size @yaxis label () @TYPE xy 0 0.000 128.385 2 7.135 3 1.552 4 0.447 5 0.120 6 0.034 7 0.009 8 0.003 9 0.001 10 0.000 11 0.000 12 0.000 -- 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 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- 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 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] trouble diagnosing a simulation that's blowing up (shake not converging -- segmentation fault)
Hello, I'm attempting to simulate ice ih in a triclinic box with a rigid tip4p water model. As the subject says, I get warnings (almost immediately) that shake failed to converge in 1000 steps and then eventually a segmentation fault. Gromacs documentation suggests that this is a result of my simulation blowing up. I tried decreasing the timestep down to 0.0001 ps, lowering the temperature, and minimizing further (down to 100 kJ/mol/nm) but nothing worked. I mostly used modified versions of the files available on this page: http://www.sklogwiki.org/SklogWiki/index.php/GROMACS_files_for_the_TIP4P/2005_model except the .gro file, which is my own. I did comment out the pressure coupling algorithms because I got a note that the barostat was unsuitable for equillibration, but I want NVT anyway. The temperature is 120.0 K and the coulomb type is PME. I've double checked and am satisfied with the interaction parameters in the topology file, so I'm out of ideas on where my mistake migh! t be. Here are the commands and files I used, in case it helps: gmx grompp -f minim.mdp -c water_5100.gro -p water_topol.top -o em.tpr gmx mdrun -v -deffnm em gmx grompp -f water_5100.mdp -c em.gro -p water_topol.top -o water.tpr gmx mdrun -deffnm water Here is the minim.mdp file: http://textuploader.com/iggv The water_topol.top file: http://textuploader.com/igpd And the water_5100.mdp file: http://textuploader.com/igzj You'll notice a slight mistake in the naming convention. There are 1700 molecules in the simulation, but everything is named something like '..._5100', even though tip4p water has a virtual site (making 4 particles). My .gro file does in fact have 6800 atoms, not 5100, I just neglected to rename the files because it's easier. Unfortunately I can't upload the .gro file because it's too big. I realize the problem could be there but I won't attach a large file unless it's specifically requested. Here's a sample: Triclinic Frozen Water Simulation 6800 1WATER OW1 0.261 0.000 0.000 0. 0. 0. 1WATER HW2 0.261 0.000 0.082 0. 0. 0. 1WATER HW3 0.343 -0.000 -0.027 0. 0. 0. 1WATER DW4 0.272 0.000 0.007 0. 0. 0. 2WATER OW5 0.261 0.000 0.736 0. 0. 0. 2WATER HW6 0.261 0.000 0.818 0. 0. 0. 2WATER HW7 0.343 0.000 0.709 0. 0. 0. 2WATER DW8 0.272 0.000 0.743 0. 0. 0. 3WATER OW9 0.261 0.000 1.472 0. 0. 0. 3WATER HW 10 0.261 0.000 1.554 0. 0. 0. 3WATER HW 11 0.343 0.000 1.445 0. 0. 0. 3WATER DW 12 0.272 0.000 1.479 0. 0. 0. 4WATER OW 13 0.261 0.000 2.208 0. 0. 0. 4WATER HW 14 0.261 0.000 2.290 0. 0. 0. 4WATER HW 15 0.343 0.000 2.181 0. 0. 0. 4WATER DW 16 0.272 0.000 2.215 0. 0. 0. 5WATER OW 17 0.261 0.000 2.944 0. 0. 0. 5WATER HW 18 0.261 0.000 3.026 0. 0. 0. 5WATER HW 19 0.343 0.000 2.917 0. 0. 0. 5WATER DW 20 0.272 0.000 2.951 0. 0. 0. 6WATER OW 21 -0.130 0.677 0.000 0. 0. 0. 6WATER HW 22 -0.130 0.677 0.082 0. 0. 0. 6WATER HW 23 -0.048 0.677 -0.027 0. 0. 0. 6WATER DW 24 -0.119 0.677 0.007 0. 0. 0. . . . . . . 1696WATER OW 6781 1.825 3.160 0.276 0. 0. 0. 1696WATER HW 6782 1.784 3.232 0.304 0. 0. 0. 1696WATER HW 6783 1.907 3.161 0.304 0. 0. 0. 1696WATER DW 6784 1.830 3.170 0.283 0. 0. 0. 1697WATER OW 6785 1.825 3.160 1.012 0. 0. 0. 1697WATER HW 6786 1.784 3.232 1.040 0. 0. 0. 1697WATER HW 6787 1.907 3.161 1.040 0. 0. 0. 1697WATER DW 6788 1.830 3.170 1.019 0. 0. 0. 1698WATER OW 6789 1.825 3.160 1.748 0. 0. 0. 1698WATER HW 6790 1.784 3.232 1.776 0. 0. 0. 1698WATER HW 6791 1.907 3.161 1.776 0. 0. 0. 1698WATER DW 6792 1.830 3.170 1.755 0. 0. 0. 1699WATER OW 6793 1.825 3.160 2.484 0. 0. 0. 1699WATER HW 6794 1.784 3.232 2.512 0. 0. 0. 1699WATER HW 6795 1.907 3.161 2.512 0. 0. 0. 1699WATER DW 6796 1.830 3.170 2.491 0. 0. 0. 1700WATER OW 6797 1.825 3.160 3.220 0. 0. 0. 1700WATER HW 6798 1.784 3.232 3.248 0. 0. 0. 1700WATER HW 6799 1.907 3.161 3.248 0. 0. 0. 1700WATER
[gmx-users] question
Dear gromacs users I am doing md simulation of protein-ligand using 5.0 version of gromacs. I want to use prodrg server for my ligand. Based on Justin's opinion, the charges should be modified. The structure of my ligand is in a way that I can't use charge of the functional groups being in aminoacids or nucleic acids in gromos force fields. I am going to obtain the charges from gaussian software. But I don't know how to set charge groups and charge group numbers to satisfy gromos force field (we have to keep groups of atoms with total charge 0 together) Please guide me about this. Best wishes, Atila -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Building gromacs on CRAY XC40
Dear Gromacs users, I am trying to build gromacs on our latest supercomputer CRAY XC40, but I am unable to do so because of lack of administrator privileges and different programming environment, w.r.t. my previous experience on tyrone supercomputers. I continuously get errors regarding something or the other, but trying to solve that results in another error. I am sure many of you would have already build gromacs on cray machines, and hence would be really grateful, if anyone can tell me the correct sequence of steps to build gromacs. I have extensively searched through the web, and documentation and nothing seems to work. It be also really great if someone could give me the link to the any thread that addresses this problem. Thanx in advance. -- Yours sincerely, Sabyasachi Sahoo -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] How to justify when the trajectory reached equilibrium
Hi, I did a 70-ns MD simulation. I wonder how to justify when the trajectory reached equilibrium... Seen from RMSD-time curve of C-alpha, the curve reached about 1 nm at 12 ns and kept stable after that. Could I justify that the system reached equilibrium at 12 ns? Are there any methods/criteria to justify the equilibrium other than RMSD evolution? Thanks a lot, Qing -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Building gromacs on CRAY XC40
Hi, your not saying what version you are trying to install. Assuming 5.0.5 it should just work with cmake -DGMX_BUILD_SHARED_EXE=off .. Make sure to select GCC or ICC as compiler with a command such as (might be different on your machine) module swap PrgEnv-pgi PrgEnv-gnu If it still doesn't work, send your exact steps and errors. Roland On Tue, Jul 7, 2015 at 1:02 AM, Sabyasachi Sahoo ssahoo.i...@gmail.com wrote: Dear Gromacs users, I am trying to build gromacs on our latest supercomputer CRAY XC40, but I am unable to do so because of lack of administrator privileges and different programming environment, w.r.t. my previous experience on tyrone supercomputers. I continuously get errors regarding something or the other, but trying to solve that results in another error. I am sure many of you would have already build gromacs on cray machines, and hence would be really grateful, if anyone can tell me the correct sequence of steps to build gromacs. I have extensively searched through the web, and documentation and nothing seems to work. It be also really great if someone could give me the link to the any thread that addresses this problem. Thanx in advance. -- Yours sincerely, Sabyasachi Sahoo -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Energy contribution of individual residues
IIRC, you do not need to redo the whole run. You can specify the new energygrps in the mdp file and use mdrun -rerun to re-process the results you already have. Check the manual for the exact syntax. Hope this helps Victor 2015-07-02 23:50 GMT-05:00 Dr. Seema Mishra seema_...@yahoo.com: Hello Gromacs users, I have run several 50 ns production runs using Gromacs. Can anyone tell me how to calculate interaction energy of indvidual protein residues with ligand? I had set energygrps as Protein LIG (LIG for ligand). I have gone through the archives, but these do not tell much and say that the results may not be accurate, and because of shortage of time, I cannot do the production run again with setting energygrps for individual residues. Do you happen to know any other good tool? Thanks. --- -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] monitor the size of the computational box
Dear all, I would like to ask what is the best way to monitor the size of the computational box (i.e. the volume) during a simulation. I know that it must stay constant during the simulation but, in my case, it seems that it doesn't. There is an error poping up when I try to use the gmx hbond tool, specifically Your computational box has shrunk too much, and I've read that it is reccomended to plot the box volume as a function of time. How can I do this? Thanking you in advance, John G. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] monitor the size of the computational box
On 7/6/15 11:15 AM, Giannis Gl wrote: Dear all, I would like to ask what is the best way to monitor the size of the computational box (i.e. the volume) during a simulation. I know that it must stay constant during the simulation but, in my case, it seems that it doesn't. The box is only constant with NVE or NVT, but with NPT it will not be. There is an error poping up when I try to use the gmx hbond tool, specifically Your computational box has shrunk too much, and I've read that it is reccomended to plot the box volume as a function of time. How can I do this? Extract it from the .edr file. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
