Re: [gmx-users] How to run pdb2gmx with -ter flag?
Hi, Now I have GROMACS v 5.0. What option should I select for -chainsep? -chainsep enum (id_or_ter) Condition in PDB files when a new chain should be started (adding termini): id_or_ter, id_and_ter, ter, id, interactive Should I change something in my PDB file? This is not clear for me. Thank you for your help Urszula Hi, -ter does not solve this problem. You should not start new work with such an old version of GROMACS; I forget when we added -chainsep, but it solves this problem. Mark On Wed, 6 May 2015 15:37 Urszula Uciechowska urszula.uciechow...@biotech.ug.edu.pl wrote: Hi, I have problems with using -tar flag in pdb2gmx, after running pdb2gmx -f COM-oH.pdb -o COM-oH.gro -p COM-oH.top -ter -ignh -water tip3p I do not get any errors however after generating a pdb using editconf I am getting a complex where the receptors are connected with bonds. What I am doing wrong? I have also tried to put the ter cards in my pdb (COM-oH.pdb): ATOM 2779 O2 DC3 136 96.011 58.127 145.405 1.00 0.00 O ATOM 2780 C3' DC3 136 94.583 61.640 142.148 1.00 0.00 C ATOM 2781 C2' DC3 136 95.682 60.578 142.176 1.00 0.00 C ATOM 2782 O3' DC3 136 94.914 62.682 143.055 1.00 0.00 O ter ATOM 2784 N MET 137 -55.937 52.177 172.707 1.00 0.00 N ATOM 2785 CA MET 137 -57.391 52.043 172.937 1.00 0.00 C ATOM 2786 CB MET 137 -58.028 53.416 173.205 1.00 0.00 C but after running pdb2gmx I am getting an error message: --- Program pdb2gmx, VERSION 4.5.3 Source code file: pdb2gmx.c, line: 655 Fatal error: Atom OXT in residue ARG 421 was not found in rtp entry ARG with 24 atoms while sorting atoms. . For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- How to run it correctly? Urszula Uciechowska University of Gdansk and Medical Univesity of Gdansk Department of Molecular and Cellular Biology ul. Kladki 24 80-822 Gdansk Poland - Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego http://www.ug.edu.pl/ -- 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. University of Gdansk and Medical Univesity of Gdansk Department of Molecular and Cellular Biology ul. Kladki 24 80-822 Gdansk Poland - Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego http://www.ug.edu.pl/ -- 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] Issue with nrexcl (g_rdf related)
Dear all, A little context first: I have written my own CG bead necklace model for use with gromacs. Production simulations use nrexcl = 1. One of the validation analysis involves computing the rdf, and for that I need a .tpr with higher nrexcl, as suggested in the tool's help. Interestingly, two different .tpr files compiled using two similar topologies, differing only on the nrexcl, produce similar outputs when checked with gmxdump (the init. velocities differ but that's normal, because the seed is random). Needless to say that rdf outputs are similar regardless of which .tpr I use (they are the same!). I double checked that the .top files differ uniquely on the nrexcl value. Tested with gmx-4.6.7 and gmx-5.0.4. P.S.: I use an harmonic potential for the bonds (func. type 6). Don't know if this matters, but I have a feeling it does. Thank you for your attention, Best regards, João Henriques -- 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] gromacs-5.0.4 installation problem
Gromacs only notified you about turning off the GPU code, that was not an error. The error was the AVX vs. SSE4.1 problem. Not sure why you are getting that since I thought cmake would get these things straight. Chris. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of James Lord jjamesgreen...@gmail.com Sent: 07 May 2015 14:05 To: gmx-us...@gromacs.org Subject: [gmx-users] gromacs-5.0.4 installation problem Hi all, I just installed a fresh ubuntu 14.04, and want to go ahead with gromacs-5.0.4 installation, I am constantly getting this annoying message, anyone can help? root@ubuntu:~/gromacs-5.0.4/build# cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -- No compatible CUDA toolkit found (v4.0+), disabling native GPU acceleration CMake Error at cmake/gmxTestSimd.cmake:220 (message): Cannot find AVX compiler flag. Use a newer compiler, or choose SSE4.1 SIMD (slower). Call Stack (most recent call first): CMakeLists.txt:716 (gmx_test_simd) -- Configuring incomplete, errors occurred! See also /home/james/gromacs-5.0.4/build/CMakeFiles/CMakeOutput.log. See also /home/james/gromacs-5.0.4/build/CMakeFiles/CMakeError.log. After this I did sudo apt-get install nvidia-cuda-toolkit but still i am getting the same message Any comments? 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.
[gmx-users] Distance Restraints
I have a two peptide system with my second chain B having as part of its topology file (and sequence) a Zinc ion. That is, the Zinc ion is literally part of the chain so, that when I generate my itp files using pdb2gmx I get topol_proteinA.itp, topol_proteinB.itp (i.e. no topol_Ion.itp)...I do this because the distance restraint I want is between the Zinc and its coordinated sulfur atoms. I believe I need the Zn and the Cys SG atoms part of the same molecule...here, chainB. I have read the distance restraint info. in the manual 4.5.4; however, I am still unsure about how to implement it. I have gotten to the point where I use genrestr to generated the itp file having the distance restraint matrix. Now, when I #include this (restraint) file in the topology.top or in the topol_proteinB.itp, I get an error saying that the restraint file is in the wrong location when I use the grompp to make a tpr file.I have also place in disre_fc = 1000 in my mdp file Can someone be explicit about what I am doing wrong...I did get the position restraint to work, but am having trouble here. Thanks, Steve -- 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-5.0.4 installation problem
Hi all, I just installed a fresh ubuntu 14.04, and want to go ahead with gromacs-5.0.4 installation, I am constantly getting this annoying message, anyone can help? root@ubuntu:~/gromacs-5.0.4/build# cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -- No compatible CUDA toolkit found (v4.0+), disabling native GPU acceleration CMake Error at cmake/gmxTestSimd.cmake:220 (message): Cannot find AVX compiler flag. Use a newer compiler, or choose SSE4.1 SIMD (slower). Call Stack (most recent call first): CMakeLists.txt:716 (gmx_test_simd) -- Configuring incomplete, errors occurred! See also /home/james/gromacs-5.0.4/build/CMakeFiles/CMakeOutput.log. See also /home/james/gromacs-5.0.4/build/CMakeFiles/CMakeError.log. After this I did sudo apt-get install nvidia-cuda-toolkit but still i am getting the same message Any comments? 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.
Re: [gmx-users] gromacs-5.0.4 installation problem
Hi Mark,Szilard and Christopher, Thanks for the comments, apparently gcc 4.8.2 is there. Really can't understand why and what it is complaining about, root@ubuntu:~/gromacs-5.0.4/build# gcc --version gcc (Ubuntu 4.8.2-19ubuntu1) 4.8.2 Copyright (C) 2013 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. So are you guys saying that a new installation might be better than messing around with this? Cheers James On Thu, May 7, 2015 at 7:21 PM, Szilárd Páll pall.szil...@gmail.com wrote: Something is strange about that Ubuntu installation, gcc 4.8.2 should be the default. -- Szilárd On Fri, May 8, 2015 at 12:10 AM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, The error means you need a newer compiler in order to take advantage of your hardware, e.g. the latest version of gcc you can get (which will probably require you add a new PPA), though I am surprised that cmake found a C++ compiler on 14.04 and then didn't find AVX support in it... something seems strange. Mark On Thu, May 7, 2015 at 8:46 PM Christopher Neale chris.ne...@alum.utoronto.ca wrote: Gromacs only notified you about turning off the GPU code, that was not an error. The error was the AVX vs. SSE4.1 problem. Not sure why you are getting that since I thought cmake would get these things straight. Chris. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of James Lord jjamesgreen...@gmail.com Sent: 07 May 2015 14:05 To: gmx-us...@gromacs.org Subject: [gmx-users] gromacs-5.0.4 installation problem Hi all, I just installed a fresh ubuntu 14.04, and want to go ahead with gromacs-5.0.4 installation, I am constantly getting this annoying message, anyone can help? root@ubuntu:~/gromacs-5.0.4/build# cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -- No compatible CUDA toolkit found (v4.0+), disabling native GPU acceleration CMake Error at cmake/gmxTestSimd.cmake:220 (message): Cannot find AVX compiler flag. Use a newer compiler, or choose SSE4.1 SIMD (slower). Call Stack (most recent call first): CMakeLists.txt:716 (gmx_test_simd) -- Configuring incomplete, errors occurred! See also /home/james/gromacs-5.0.4/build/CMakeFiles/CMakeOutput.log. See also /home/james/gromacs-5.0.4/build/CMakeFiles/CMakeError.log. After this I did sudo apt-get install nvidia-cuda-toolkit but still i am getting the same message Any comments? 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. -- 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] gromacs-5.0.4 installation problem
Hi, please rerun cmake from an empty build directly and post both the full cmake output and the content of CMakeFiles/CMakeError.log. Roland On Thu, May 7, 2015 at 7:38 PM, James Lord jjamesgreen...@gmail.com wrote: Hi Mark,Szilard and Christopher, Thanks for the comments, apparently gcc 4.8.2 is there. Really can't understand why and what it is complaining about, root@ubuntu:~/gromacs-5.0.4/build# gcc --version gcc (Ubuntu 4.8.2-19ubuntu1) 4.8.2 Copyright (C) 2013 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. So are you guys saying that a new installation might be better than messing around with this? Cheers James On Thu, May 7, 2015 at 7:21 PM, Szilárd Páll pall.szil...@gmail.com wrote: Something is strange about that Ubuntu installation, gcc 4.8.2 should be the default. -- Szilárd On Fri, May 8, 2015 at 12:10 AM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, The error means you need a newer compiler in order to take advantage of your hardware, e.g. the latest version of gcc you can get (which will probably require you add a new PPA), though I am surprised that cmake found a C++ compiler on 14.04 and then didn't find AVX support in it... something seems strange. Mark On Thu, May 7, 2015 at 8:46 PM Christopher Neale chris.ne...@alum.utoronto.ca wrote: Gromacs only notified you about turning off the GPU code, that was not an error. The error was the AVX vs. SSE4.1 problem. Not sure why you are getting that since I thought cmake would get these things straight. Chris. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of James Lord jjamesgreen...@gmail.com Sent: 07 May 2015 14:05 To: gmx-us...@gromacs.org Subject: [gmx-users] gromacs-5.0.4 installation problem Hi all, I just installed a fresh ubuntu 14.04, and want to go ahead with gromacs-5.0.4 installation, I am constantly getting this annoying message, anyone can help? root@ubuntu:~/gromacs-5.0.4/build# cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -- No compatible CUDA toolkit found (v4.0+), disabling native GPU acceleration CMake Error at cmake/gmxTestSimd.cmake:220 (message): Cannot find AVX compiler flag. Use a newer compiler, or choose SSE4.1 SIMD (slower). Call Stack (most recent call first): CMakeLists.txt:716 (gmx_test_simd) -- Configuring incomplete, errors occurred! See also /home/james/gromacs-5.0.4/build/CMakeFiles/CMakeOutput.log. See also /home/james/gromacs-5.0.4/build/CMakeFiles/CMakeError.log. After this I did sudo apt-get install nvidia-cuda-toolkit but still i am getting the same message Any comments? 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. -- 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. -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL
Re: [gmx-users] Constraint of active site in gromacs
On 5/7/15 6:33 AM, Raj D wrote: Dear Mark, So to make distance restrain of specific atoms of protein residues and the ligand (itp file produced by antechamber), I may have to cut the ligating atoms of amino acids in the topology as produced by pdb2gmx and paste into the ligand.itp to make the distance restraint to work ...Is it the right approach to bring all distance restrained atoms to bring into the same molecule type ? You can't have a separate ligand topology for this to work. It literally needs to be a merged [moleculetype] for everything that will participate in distance restraints. That requires creation of an .rtp entry (not .itp file) for pdb2gmx to use in creating the topology, in concert with the -merge option. -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.
Re: [gmx-users] Constraint of active site in gromacs
On 5/7/15 8:13 AM, Raj D wrote: Thanks Justin, Is there any tool to convert itp file contents to gromacs formated ff file ? Not that I'm aware of, but it's a simple exercise. You have the hard part (parametrization) done. Now you just need to write the .rtp entry. See Chapter 5 and the existing entries for format. -Justin On May 7, 2015 5:23 PM, Justin Lemkul jalem...@vt.edu wrote: On 5/7/15 6:33 AM, Raj D wrote: Dear Mark, So to make distance restrain of specific atoms of protein residues and the ligand (itp file produced by antechamber), I may have to cut the ligating atoms of amino acids in the topology as produced by pdb2gmx and paste into the ligand.itp to make the distance restraint to work ...Is it the right approach to bring all distance restrained atoms to bring into the same molecule type ? You can't have a separate ligand topology for this to work. It literally needs to be a merged [moleculetype] for everything that will participate in distance restraints. That requires creation of an .rtp entry (not .itp file) for pdb2gmx to use in creating the topology, in concert with the -merge option. -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.
[gmx-users] gromacs 5.0 tools: gmx distance and gmx mindist time series
Dear All, I am trying to use the new gromacs 5.0 tools for analysis. I tried multiple options but I can't get gmx distance and gmx mindist to print out time series of distances. I only get the average. On the other hand, I had no problem with getting the time series with gromacs 4.6 g_dist and g_mindist. Don't know if it's a problem of the code or if I just don't know how to use the tool... I'd appreciate your tips! oliwia -- 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] Vacuum simulation in GMX 5
On 5/7/15 8:43 AM, Eudes Fileti wrote: Justin, thanks for the help. Originally I have tried the options you suggested, and the GMX 5 not accepted well, since there are not more -pd option, which allowed to perform the calculation with pbc = no. Well, technically it allows you to run in parallel via PD with no PBC. Parallelization is not mandatory and usually small vacuum systems do not benefit from running in parallel (usually performance degrades when you have few atoms). So, you asked me to see my input. The first test I did was obviously considering cut-offs, since I needed impose pbc = yes. These parameters are the ones I sent you. pbc = xyz is not an in vacuo simulation. Of course plain cutoffs is not dealing well with the electrostatic part, but in this case I was only doing just a quick test. You said you have made calculations for a molecule of 50 atoms at a rate of 130ns/day on a single core. Did you used to that Gromacs 5? What are the mdp options that you use in this case? Yes, version 5.0, using exactly the settings I posted. -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.
Re: [gmx-users] gromacs 5.0 tools: gmx distance and gmx mindist time series
Hi, Time series are what gmx distance does... see gmx distance -h, of course. If it's not working for you, you'll have to tell us exactly what you tried, what output you got, what's not suitable, etc., and check that your input files contain what you think they do (e.g. with gmx check) Mark On Thu, May 7, 2015 at 2:38 PM oliwias oliw...@ethz.ch wrote: Dear All, I am trying to use the new gromacs 5.0 tools for analysis. I tried multiple options but I can't get gmx distance and gmx mindist to print out time series of distances. I only get the average. On the other hand, I had no problem with getting the time series with gromacs 4.6 g_dist and g_mindist. Don't know if it's a problem of the code or if I just don't know how to use the tool... I'd appreciate your tips! oliwia -- 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] Verlet and Energy Groups
Does anyone know when the cutoff scheme verlet will support energy groups so one could monitor L-J and columbic interactions between groups. I am using the developer version of Gromacs 5. Thanks Jarrett -- 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] Vacuum simulation in GMX 5
Justin, thanks for the help. Originally I have tried the options you suggested, and the GMX 5 not accepted well, since there are not more -pd option, which allowed to perform the calculation with pbc = no. So, you asked me to see my input. The first test I did was obviously considering cut-offs, since I needed impose pbc = yes. These parameters are the ones I sent you. Of course plain cutoffs is not dealing well with the electrostatic part, but in this case I was only doing just a quick test. You said you have made calculations for a molecule of 50 atoms at a rate of 130ns/day on a single core. Did you used to that Gromacs 5? What are the mdp options that you use in this case? eef ___ Eudes Eterno Fileti Instituto de Ciência e Tecnologia da UNIFESP Rua Talim, 330, São José dos Campos - SP Página: sites.google.com/site/fileti/ -- 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] Constraint of active site in gromacs
Dear Mark, So to make distance restrain of specific atoms of protein residues and the ligand (itp file produced by antechamber), I may have to cut the ligating atoms of amino acids in the topology as produced by pdb2gmx and paste into the ligand.itp to make the distance restraint to work ...Is it the right approach to bring all distance restrained atoms to bring into the same molecule type ? Regards, Raja So Thanks Mark, I will do that . Regards, On May 6, 2015 8:07 PM, Mark Abraham mark.j.abra...@gmail.com wrote: Yes, but you need distance restraints (not constraints, which are different) like Justin said. You also need to get both ligating water molecules, protein and ion into the same moleculetype to make that work. That's not trivial, so make sure you really need that EM for something. Mark On Wed, 6 May 2015 15:57 Raj D gromacs.fo...@gmail.com wrote: Thanks Justin , but I have a modelled protein download from Modbase and added Fe iron into the approximate ligating distance of three ligating atoms of the amino acids. Now I am aiming to bring the octahedral geometry of the Fe coordinating atoms which include two more water molecules using EM engine of Gromacs. Will it be possible to let the EM to optimize the distances between the atoms of the octahedral by constraining the angles and positions of the atom positions for a octahedral geometry ? Regards, Raja On May 6, 2015 5:14 PM, Justin Lemkul jalem...@vt.edu wrote: On 5/6/15 3:09 AM, Raj D wrote: Dear User, I would like to constraint the Iron bound active site of the protein in octahedral shape in EM and MD steps ... Is there a direct routine to create such a constraint in gromacs by feeding information of ligating atoms of amino acids with Iron at the center of the octahedral geometry. What you need are distance restraints, which you will have to write in the topology yourself. -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_Listbefore posting! * Can't post? Readhttp://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-usersor send a mail togmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_Listbefore posting! * Can't post? Readhttp://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-usersor send a mail togmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_Listbefore posting! * Can't post? Readhttp://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-usersor send a mail togmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_Listbefore posting! * Can't post? Readhttp://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-usersor send a mail togmx-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] Vacuum simulation in GMX 5 (Justin Lemkul)
Hi Justin, this is my mdp options. thanks eef ; Run control define = -DPOSRES integrator = sd ; Langevin dynamics tinit= 0 dt = 0.002 nsteps = 500; 100 ps nstcomm = 100 ; Output control nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 100 nstenergy= 100 nstxout-compressed = 0 ; Neighborsearching and short-range nonbonded interactions cutoff-scheme= verlet nstlist = 20 ns_type = grid pbc = xyz rlist= 1.2 ; Electrostatics coulombtype = cut-off rcoulomb = 1.2 ; van der Waals vdwtype = cutoff vdw-modifier = force-switch rvdw-switch = 1.0 rvdw = 1.2 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = no ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.12 ; EWALD/PME/PPPM parameters pme_order= 6 ewald_rtol = 1e-06 epsilon_surface = 0 ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling tcoupl = v-rescale nsttcouple = -1 nh-chain-length = 10 print-nose-hoover-chain-variables = no ; Groups to couple separately tc-grps = system ; Time constant (ps) and reference temperature (K) tau-t= 0.1 ref-t= 323 ; pressure coupling Pcoupl = no Pcoupltype = isotropic nstpcouple = -1 ; Time constant (ps), compressibility (1/bar) and reference P (bar) tau-p= 2.0 compressibility = 4.5e-5 ref-p= 1.0 ; Scaling of reference coordinates, No, All or COM refcoord-scaling = com ; Free energy control stuff free_energy = yes init_lambda_state= 0 delta_lambda = 0 calc_lambda_neighbors= 1; only immediate neighboring windows vdw_lambdas = 0.00 0.00 0.00 0... .70 0.75 0.80 0.85 0.90 0.95 1.00 coul_lambdas = 0.00 0.05 0.10 01.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 ; Options for the decoupling sc-alpha = 0.5 sc-coul = no ; linear interpolation of Coulomb (none in this case) sc-power = 1.0 sc-sigma = 0.3 couple-moltype = Pept ; name of moleculet ype to decouple couple-lambda0 = vdw-q ; only van der Waals interactions couple-lambda1 = none ; turn off everything, in this case only vdW couple-intramol = yes nstdhdl = 10 ; Generate velocities to start gen_vel = yes gen_temp = 300 gen_seed = -1 ; options for bonds constraints = h-bonds ; we only have C-H bonds here ; Type of constraint algorithm constraint-algorithm = lincs ; Do not constrain the starting configuration continuation = no ; Highest order in the expansion of the constraint coupling matrix lincs-order = 12 ___ Eudes Eterno Fileti Instituto de Ciência e Tecnologia da UNIFESP Rua Talim, 330, São José dos Campos - SP Página: sites.google.com/site/fileti/ On 6 May 2015 at 14:04, gromacs.org_gmx-users-requ...@maillist.sys.kth.se wrote: Send gromacs.org_gmx-users mailing list submissions to gromacs.org_gmx-users@maillist.sys.kth.se To subscribe or unsubscribe via the World Wide Web, visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or, via email, send a message with subject or body 'help' to gromacs.org_gmx-users-requ...@maillist.sys.kth.se You can reach the person managing the list at gromacs.org_gmx-users-ow...@maillist.sys.kth.se When replying, please edit your Subject line so it is more specific than Re: Contents of gromacs.org_gmx-users digest... Today's Topics: 1. Re: Constraint of active site in gromacs (Mark Abraham) 2. Re: Constraint of active site in gromacs (Nataraj Balakrishnan) 3. on a MD run notice (Brett) 4. Re: on a MD run notice (Justin Lemkul) 5. Vacuum simulation in GMX 5 (Eudes Fileti) 6. Re: Vacuum simulation in GMX 5 (Justin Lemkul) -- -- Message: 5 Date: Wed, 6 May 2015 13:54:28 -0300 From: Eudes Fileti fil...@gmail.com To: gmx-us...@gromacs.org Subject: [gmx-users] Vacuum simulation in GMX 5 Message-ID: CAHC5Q= gbdfnhmxhnzcpditqelxmsfpqig9uf-ck3c+rjsck...@mail.gmail.com Content-Type: text/plain; charset=UTF-8 Hello, in the previous gmx versions I could accelerate simulations in vacuum making the cutting cut-offs zero
[gmx-users] how to avoid multiple 'aprun' on batch job script?
Dear All,
Currently I am running simulation using Gromac-5.0.4 on Cray XC40.
Its a protein in water system (100K), 300K, NPT ensemble, writing full
precision output in every 2ps and compressed trajectory in 1ps.
I have divided the run into 2ns bin, and the following command is used in
a loop to run the job starting from 2ns:
loop
aprun -n 144 -N 24 -j1 gmx_mpi mdrun -cpi simu-$nt-to-$nt1.cpt -deffnm
simu-$nt1-to-$nt2
loop
(aprun -n 144 -N 24 -j1 gmx_mpi mdrun -cpi simu-0-to-2.cpt -deffnm
simu-2-to-4)
('tpr' files are generated by 'convert-tpr' program:
gmx convert-tpr -s simu-0-to-2.tpr -o simu-2-to-4.tpr -extend 2000)
Kindly suggest better way of doing this, if any.
Since it is running on a loop, I need to invoke 'aprun' on every 2ns steps.
Is it possible to run the loop by using 'aprun' only once?
My admin is insisting to avoid multiple 'aprun' command on same job script.
Please help.
With best regards,
Satyabrata Das
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Re: [gmx-users] gromacs-5.0.4 installation problem
YAY :-) it is working, Do not know what was wrong but apparently something was seriously messed up with cmake and compilers, removed cmake and gcc gcc++ complier and gromacs, re-doing solved the problem. *sudo apt-get update -y* *sudo apt-get update**sudo apt-get install cmake* Cheers James On Thu, May 7, 2015 at 7:45 PM, Roland Schulz rol...@utk.edu wrote: Hi, please rerun cmake from an empty build directly and post both the full cmake output and the content of CMakeFiles/CMakeError.log. Roland On Thu, May 7, 2015 at 7:38 PM, James Lord jjamesgreen...@gmail.com wrote: Hi Mark,Szilard and Christopher, Thanks for the comments, apparently gcc 4.8.2 is there. Really can't understand why and what it is complaining about, root@ubuntu:~/gromacs-5.0.4/build# gcc --version gcc (Ubuntu 4.8.2-19ubuntu1) 4.8.2 Copyright (C) 2013 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. So are you guys saying that a new installation might be better than messing around with this? Cheers James On Thu, May 7, 2015 at 7:21 PM, Szilárd Páll pall.szil...@gmail.com wrote: Something is strange about that Ubuntu installation, gcc 4.8.2 should be the default. -- Szilárd On Fri, May 8, 2015 at 12:10 AM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, The error means you need a newer compiler in order to take advantage of your hardware, e.g. the latest version of gcc you can get (which will probably require you add a new PPA), though I am surprised that cmake found a C++ compiler on 14.04 and then didn't find AVX support in it... something seems strange. Mark On Thu, May 7, 2015 at 8:46 PM Christopher Neale chris.ne...@alum.utoronto.ca wrote: Gromacs only notified you about turning off the GPU code, that was not an error. The error was the AVX vs. SSE4.1 problem. Not sure why you are getting that since I thought cmake would get these things straight. Chris. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of James Lord jjamesgreen...@gmail.com Sent: 07 May 2015 14:05 To: gmx-us...@gromacs.org Subject: [gmx-users] gromacs-5.0.4 installation problem Hi all, I just installed a fresh ubuntu 14.04, and want to go ahead with gromacs-5.0.4 installation, I am constantly getting this annoying message, anyone can help? root@ubuntu:~/gromacs-5.0.4/build# cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -- No compatible CUDA toolkit found (v4.0+), disabling native GPU acceleration CMake Error at cmake/gmxTestSimd.cmake:220 (message): Cannot find AVX compiler flag. Use a newer compiler, or choose SSE4.1 SIMD (slower). Call Stack (most recent call first): CMakeLists.txt:716 (gmx_test_simd) -- Configuring incomplete, errors occurred! See also /home/james/gromacs-5.0.4/build/CMakeFiles/CMakeOutput.log. See also /home/james/gromacs-5.0.4/build/CMakeFiles/CMakeError.log. After this I did sudo apt-get install nvidia-cuda-toolkit but still i am getting the same message Any comments? 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. -- 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
Re: [gmx-users] Constraint of active site in gromacs
Thanks Justin . I will try it. On May 7, 2015 5:48 PM, Justin Lemkul jalem...@vt.edu wrote: On 5/7/15 8:13 AM, Raj D wrote: Thanks Justin, Is there any tool to convert itp file contents to gromacs formated ff file ? Not that I'm aware of, but it's a simple exercise. You have the hard part (parametrization) done. Now you just need to write the .rtp entry. See Chapter 5 and the existing entries for format. -Justin On May 7, 2015 5:23 PM, Justin Lemkul jalem...@vt.edu wrote: On 5/7/15 6:33 AM, Raj D wrote: Dear Mark, So to make distance restrain of specific atoms of protein residues and the ligand (itp file produced by antechamber), I may have to cut the ligating atoms of amino acids in the topology as produced by pdb2gmx and paste into the ligand.itp to make the distance restraint to work ...Is it the right approach to bring all distance restrained atoms to bring into the same molecule type ? You can't have a separate ligand topology for this to work. It literally needs to be a merged [moleculetype] for everything that will participate in distance restraints. That requires creation of an .rtp entry (not .itp file) for pdb2gmx to use in creating the topology, in concert with the -merge option. -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. -- 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] gromacs 5.0 tools: gmx distance and gmx mindist time series
Hi Mark, I'm quite new to gromacs, so thanks for your help! I have an md trajectory in 3 files. I used: gmx_trjcat -f md1.xtc md2.xtc md3.xtc -o md.xtc -settime in order to get one file for analysis. I set the time of the first file to 0.0, and for the next two files I set the time to c (continue, I suppose). When I run: gmx check -f md.xtc -s1 md_2.tpr -c I get a message: Timesteps at t=2 don't match (2, 5) I don't know why... The only reason that comes to my mind is that between run 1 and run 2 I changed the frequency of output. Still, I don't understand why I get the time series when using the tool from gromacs 4.6 (seems that it doesn't care about the timestep mismatch), but not using gromacs 5.0? Cheers, oliwia On 07.05.2015 14:59, Mark Abraham wrote: Hi, Time series are what gmx distance does... see gmx distance -h, of course. If it's not working for you, you'll have to tell us exactly what you tried, what output you got, what's not suitable, etc., and check that your input files contain what you think they do (e.g. with gmx check) Mark On Thu, May 7, 2015 at 2:38 PM oliwias oliw...@ethz.ch wrote: Dear All, I am trying to use the new gromacs 5.0 tools for analysis. I tried multiple options but I can't get gmx distance and gmx mindist to print out time series of distances. I only get the average. On the other hand, I had no problem with getting the time series with gromacs 4.6 g_dist and g_mindist. Don't know if it's a problem of the code or if I just don't know how to use the tool... I'd appreciate your tips! oliwia -- 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] n2t file format for similar atoms
Okay, that sounds good. Thank you! Jon On 5/6/15 1:22 PM, jwill...@andrew.cmu.edu wrote: Hello, I'm trying to specify two different hydroxyl hydrogen atoms in the n2t format: Hopls_9880.435 1.0079 1O 0.0945 and Hopls_1170.4238 1.008 1 O 0.1 for a hydroxyl group on graphene and water, respectively. When performing x2top, it seems to assume all Hs in the system are defined by whichever set of parameters is listed first. I tried using alternate atom labels, e.g. HG and HW, but it gave the same problem. Is there a way to separate the two different hydrogen types? The simplest approach is to not use x2top for writing a water topology. It should be straightforward to write the water topology and #include it in the .top (or simply use one of the existing models). Likely what's happening is that x2top is matching the first instance of any H that matches the distance criterion (within 10% of the specified distance). I bet if you reverse the appearance of the H lines in the .n2t, you'd get the opposite parameters assigned. You could modify the x2top code to be more permissive if you like, but the simplest solution is what I said above - don't ask x2top to do something complex when the molecule isn't complex :) -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] gromacs-5.0.4 installation problem
Hi, The error means you need a newer compiler in order to take advantage of your hardware, e.g. the latest version of gcc you can get (which will probably require you add a new PPA), though I am surprised that cmake found a C++ compiler on 14.04 and then didn't find AVX support in it... something seems strange. Mark On Thu, May 7, 2015 at 8:46 PM Christopher Neale chris.ne...@alum.utoronto.ca wrote: Gromacs only notified you about turning off the GPU code, that was not an error. The error was the AVX vs. SSE4.1 problem. Not sure why you are getting that since I thought cmake would get these things straight. Chris. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of James Lord jjamesgreen...@gmail.com Sent: 07 May 2015 14:05 To: gmx-us...@gromacs.org Subject: [gmx-users] gromacs-5.0.4 installation problem Hi all, I just installed a fresh ubuntu 14.04, and want to go ahead with gromacs-5.0.4 installation, I am constantly getting this annoying message, anyone can help? root@ubuntu:~/gromacs-5.0.4/build# cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -- No compatible CUDA toolkit found (v4.0+), disabling native GPU acceleration CMake Error at cmake/gmxTestSimd.cmake:220 (message): Cannot find AVX compiler flag. Use a newer compiler, or choose SSE4.1 SIMD (slower). Call Stack (most recent call first): CMakeLists.txt:716 (gmx_test_simd) -- Configuring incomplete, errors occurred! See also /home/james/gromacs-5.0.4/build/CMakeFiles/CMakeOutput.log. See also /home/james/gromacs-5.0.4/build/CMakeFiles/CMakeError.log. After this I did sudo apt-get install nvidia-cuda-toolkit but still i am getting the same message Any comments? 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. -- 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] gromacs-5.0.4 installation problem
Something is strange about that Ubuntu installation, gcc 4.8.2 should be the default. -- Szilárd On Fri, May 8, 2015 at 12:10 AM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, The error means you need a newer compiler in order to take advantage of your hardware, e.g. the latest version of gcc you can get (which will probably require you add a new PPA), though I am surprised that cmake found a C++ compiler on 14.04 and then didn't find AVX support in it... something seems strange. Mark On Thu, May 7, 2015 at 8:46 PM Christopher Neale chris.ne...@alum.utoronto.ca wrote: Gromacs only notified you about turning off the GPU code, that was not an error. The error was the AVX vs. SSE4.1 problem. Not sure why you are getting that since I thought cmake would get these things straight. Chris. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of James Lord jjamesgreen...@gmail.com Sent: 07 May 2015 14:05 To: gmx-us...@gromacs.org Subject: [gmx-users] gromacs-5.0.4 installation problem Hi all, I just installed a fresh ubuntu 14.04, and want to go ahead with gromacs-5.0.4 installation, I am constantly getting this annoying message, anyone can help? root@ubuntu:~/gromacs-5.0.4/build# cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -- No compatible CUDA toolkit found (v4.0+), disabling native GPU acceleration CMake Error at cmake/gmxTestSimd.cmake:220 (message): Cannot find AVX compiler flag. Use a newer compiler, or choose SSE4.1 SIMD (slower). Call Stack (most recent call first): CMakeLists.txt:716 (gmx_test_simd) -- Configuring incomplete, errors occurred! See also /home/james/gromacs-5.0.4/build/CMakeFiles/CMakeOutput.log. See also /home/james/gromacs-5.0.4/build/CMakeFiles/CMakeError.log. After this I did sudo apt-get install nvidia-cuda-toolkit but still i am getting the same message Any comments? 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. -- 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] Issue with nrexcl (g_rdf related)
Dear all, Please ignore my previous email. I have now realized that a bond with func. type 1 will solve my problem and keep the model intact. It's also an harmonic potential but considers exclusions. Best regards, João Henriques On Thu, May 7, 2015 at 10:23 AM, João Henriques joao.henriques.32...@gmail.com wrote: Dear all, A little context first: I have written my own CG bead necklace model for use with gromacs. Production simulations use nrexcl = 1. One of the validation analysis involves computing the rdf, and for that I need a .tpr with higher nrexcl, as suggested in the tool's help. Interestingly, two different .tpr files compiled using two similar topologies, differing only on the nrexcl, produce similar outputs when checked with gmxdump (the init. velocities differ but that's normal, because the seed is random). Needless to say that rdf outputs are similar regardless of which .tpr I use (they are the same!). I double checked that the .top files differ uniquely on the nrexcl value. Tested with gmx-4.6.7 and gmx-5.0.4. P.S.: I use an harmonic potential for the bonds (func. type 6). Don't know if this matters, but I have a feeling it does. Thank you for your attention, Best regards, João Henriques -- 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 4.6.7 with MPI and OpenMP
All, I'm attempting to build gromacs on a new cluster and following the same recipies that I've used in the past, but encountering a strange behavior: It claims to be using both MPI and OpenMP, but I can see by 'top' and the reported core/walltime that it's really only generating the MPI processes and no threads. We're running a hetergenous environment, so I tend to build with MPI/OpenMP/CUDA and the Intel compilers, but I'm seeing this same sort of behavior with the GNU compilers. Here's how I'm configuring things: [root@login01 build2]# cmake -DGMX_FFT_LIBRARY=mkl -DGMX_MPI=ON -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/opt/cuda -DGMX_OPENMP=ON -DCMAKE_INSTALL_PREFIX=/act/gromacs-4.6.7_take2 .. | tee cmake.out or with GNU: [root@login01 build2]# cmake -DGMX_BUILD_OWN_FFTW=ON -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/opt/cuda -DGMX_MPI=ON -DGMX_OPENMP=ON -DCMAKE_INSTALL_PREFIX=/act/gromacs-4.6.7_take2 .. | tee cmake.out I'm explicitly setting GMX_GPU=ON, but I don't recall having to do so in the past. I see in the output where it's testing for OpenMP: [root@login01 build]# grep OpenMP cmake.out -- Try OpenMP C flag = [-openmp] -- Performing Test OpenMP_FLAG_DETECTED -- Performing Test OpenMP_FLAG_DETECTED - Success -- Try OpenMP CXX flag = [-openmp] -- Performing Test OpenMP_FLAG_DETECTED -- Performing Test OpenMP_FLAG_DETECTED - Success -- Found OpenMP: -openmp When I go to run, I use 'mpirun -np 2' to trigger it to use 2 GPUs, then use the '-ntomp 4' flag to trigger 4 OpenMP threads/MPI proceess. The funny part is that GROMACS reports that it's doing all this: Using 2 MPI processes Using 4 OpenMP threads per MPI process although I do see this warning: Number of CPUs detected (16) does not match the number reported by OpenMP (1). I'm not sure how to proceed with debugging this, so any suggestions would be helpful. Thanks in advance, Malcolm -- Malcolm Tobias 314.362.1594 -- 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] gromacs 5.0 tools: gmx distance and gmx mindist time series
Hi, On Thu, May 7, 2015 at 3:59 PM oliwias oliw...@ethz.ch wrote: 1. How can I get rid of the inconsistency? Did I use the wrong options for gmx_trjcat? Depends whether you care. You wrote files with two different output periods, and now you want to treat them as a continuous thing, which in one sense they are not. Whether that matters depends what you want to do next, and that's your call. trjconv has functionality that would e.g. let you extract only the frames from one set of trajectories that will match the period of the other, and then you can trjcat the lot together. You can also first get gmx distance working on your partial trajectories, to solve that part of the problem independently. 2. About the distances - for gromacs 4.6.7 I used: printf A\nB\n | g_dist -s md_2.tpr -f md.xtc -n sys.ndx -o dist.xvg -dt 100 for gromacs 5.0 I used: printf A\nB\n | gmx distance -s md_2.tpr -f md.xtc -n sys.ndx -oall dist_all.xvg -oav dist_av.xvg -oh dist_h.xvg -dt 100 -tu ns You're doing two different things here. You've set the units with -tu to ns, and so (IIRC) -dt is interpreted in that context. I don't know if that's part of the problem. More important is that you read gmx distance -h, compare with g_dist -h and realise that the functionality in gmx distance is much greater than g_dist. You need to use the selection syntax to get the COM for your two index grounds, which g_dist did for you because that's all it could do. Mark Doees that indicate anything? Cheers, oliwia On 07.05.2015 15:43, Mark Abraham wrote: Hi On Thu, May 7, 2015 at 3:34 PM oliwias oliw...@ethz.ch wrote: Hi Mark, I'm quite new to gromacs, so thanks for your help! I have an md trajectory in 3 files. I used: gmx_trjcat -f md1.xtc md2.xtc md3.xtc -o md.xtc -settime in order to get one file for analysis. I set the time of the first file to 0.0, and for the next two files I set the time to c (continue, I suppose). When I run: gmx check -f md.xtc -s1 md_2.tpr -c I get a message: Timesteps at t=2 don't match (2, 5) I don't know why... The only reason that comes to my mind is that between run 1 and run 2 I changed the frequency of output. Yes, that's what the message is telling you, in case you didn't know, messed up, etc. Still, I don't understand why I get the time series when using the tool from gromacs 4.6 (seems that it doesn't care about the timestep mismatch), but not using gromacs 5.0? Neither can we, since you didn't tell us what you did when you tried to get the time series. Here you talked about how you built your inputs. Mark Cheers, oliwia On 07.05.2015 14:59, Mark Abraham wrote: Hi, Time series are what gmx distance does... see gmx distance -h, of course. If it's not working for you, you'll have to tell us exactly what you tried, what output you got, what's not suitable, etc., and check that your input files contain what you think they do (e.g. with gmx check) Mark On Thu, May 7, 2015 at 2:38 PM oliwias oliw...@ethz.ch wrote: Dear All, I am trying to use the new gromacs 5.0 tools for analysis. I tried multiple options but I can't get gmx distance and gmx mindist to print out time series of distances. I only get the average. On the other hand, I had no problem with getting the time series with gromacs 4.6 g_dist and g_mindist. Don't know if it's a problem of the code or if I just don't know how to use the tool... I'd appreciate your tips! oliwia -- 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. -- 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
Re: [gmx-users] Verlet and Energy Groups
Hi, You already can, but not when running on a GPU (because that would be slow to run). Such workflows make sense to do with mdrun -rerun outputtrajectory -nb cpu, so that you only accept the overhead of energy groups on frames for which you actually need that overhead. Mark On Thu, May 7, 2015 at 3:11 PM Jarrett Lee Wise jwi...@uwyo.edu wrote: Does anyone know when the cutoff scheme verlet will support energy groups so one could monitor L-J and columbic interactions between groups. I am using the developer version of Gromacs 5. Thanks Jarrett -- 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] Bin size for an Umbrella Sampling analysis
Dear Users, I am doing analysis for umbrella sampling and find the chosen bin size affecting the overlapping of histograms. While we should always guarantee a “well” overlapped histogram, choosing of bin size seems to have certain criteria that I did not expect before. Looking forward to any experience sharing. Regards, Kevin PhD Candidate Department of Physics and Material Science City University of Hong Kong uk...@gmx.hk -- 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] problem after installation
hello, I was at this step of the installation: GROMACS installs the script GMXRC in the bin subdirectory of the installation directory (e.g. /usr/local/gromacs/bin/GMXRC), which you should source from your shell: source /your/installation/prefix/here/bin/GMXRC It will detect what kind of shell you are running and set up your environment for using GROMACS. You may wish to arrange for your login scripts to do this automatically; please search the web for instructions on how to do this for your shell. Many of the GROMACS programs rely on data installed in the share/gromacs subdirectory of the installation directory. By default, the programs will use the environment variables set in the GMXRC script, and if this is not available they will try to guess the path based on their own location. This usually works well unless you change the names of directories inside the install tree. If you still need to do that, you might want to recompile with the new install location properly set, or edit the GMXRC script. is the GMXRC script the gmx[...].bash file? when I try source with this file nothing happens. What do I have to do, when the installation is done to run gromacs? Is there a user interface? Thanks in advance Kim J. Novacek -- 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] problem after installation
Hi, On Thu, May 7, 2015 at 1:45 PM Kim Jessica Novacek kim.j.nova...@campus.lmu.de wrote: hello, I was at this step of the installation: GROMACS installs the script GMXRC in the bin subdirectory of the installation directory (e.g. /usr/local/gromacs/bin/GMXRC), which you should source from your shell: source /your/installation/prefix/here/bin/GMXRC It will detect what kind of shell you are running and set up your environment for using GROMACS. You may wish to arrange for your login scripts to do this automatically; please search the web for instructions on how to do this for your shell. Many of the GROMACS programs rely on data installed in the share/gromacs subdirectory of the installation directory. By default, the programs will use the environment variables set in the GMXRC script, and if this is not available they will try to guess the path based on their own location. This usually works well unless you change the names of directories inside the install tree. If you still need to do that, you might want to recompile with the new install location properly set, or edit the GMXRC script. is the GMXRC script the gmx[...].bash file? when I try source with this file nothing happens. No, the GMXRC script is called GMXRC. You want a command like source /usr/local/gromacs/bin/GMXRC (or whatever is actually appropriate for where you installed it). What do I have to do, when the installation is done to run gromacs? Is there a user interface? GROMACS is a set of UNIX-style command-line programs. You might want to start with some of the material here http://www.gromacs.org/Documentation/Tutorials Mark Thanks in advance Kim J. Novacek -- 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] How to run pdb2gmx with -ter flag?
On 5/7/15 4:01 AM, Urszula Uciechowska wrote: Hi, Now I have GROMACS v 5.0. What option should I select for -chainsep? -chainsep enum (id_or_ter) Condition in PDB files when a new chain should be started (adding termini): id_or_ter, id_and_ter, ter, id, interactive Should I change something in my PDB file? This is not clear for me. Thank you for your help You seem to want TER to indicate separate chains, so the default (id_or_ter) will work, as will ter or interactive, which allows you to specifically choose which chains are to be separated. The default behavior should have been working fine without you having to do anything, so if you're getting bonds between chains, that seems very weird. Make sure you're not just assuming there are actual bonds from some bad rendering in the visualization software. The topology is definitive. What you see in VMD et al. is not. -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.
Re: [gmx-users] Constraint of active site in gromacs
Thanks Justin, Is there any tool to convert itp file contents to gromacs formated ff file ? On May 7, 2015 5:23 PM, Justin Lemkul jalem...@vt.edu wrote: On 5/7/15 6:33 AM, Raj D wrote: Dear Mark, So to make distance restrain of specific atoms of protein residues and the ligand (itp file produced by antechamber), I may have to cut the ligating atoms of amino acids in the topology as produced by pdb2gmx and paste into the ligand.itp to make the distance restraint to work ...Is it the right approach to bring all distance restrained atoms to bring into the same molecule type ? You can't have a separate ligand topology for this to work. It literally needs to be a merged [moleculetype] for everything that will participate in distance restraints. That requires creation of an .rtp entry (not .itp file) for pdb2gmx to use in creating the topology, in concert with the -merge option. -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] Vacuum simulation in GMX 5 (Justin Lemkul)
On 5/7/15 8:04 AM, Eudes Fileti wrote: Hi Justin, this is my mdp options. I'm guessing you missed my reply from yesterday: https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2015-May/097266.html -Justin thanks eef ; Run control define = -DPOSRES integrator = sd ; Langevin dynamics tinit= 0 dt = 0.002 nsteps = 500; 100 ps nstcomm = 100 ; Output control nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 100 nstenergy= 100 nstxout-compressed = 0 ; Neighborsearching and short-range nonbonded interactions cutoff-scheme= verlet nstlist = 20 ns_type = grid pbc = xyz rlist= 1.2 ; Electrostatics coulombtype = cut-off rcoulomb = 1.2 ; van der Waals vdwtype = cutoff vdw-modifier = force-switch rvdw-switch = 1.0 rvdw = 1.2 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = no ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.12 ; EWALD/PME/PPPM parameters pme_order= 6 ewald_rtol = 1e-06 epsilon_surface = 0 ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling tcoupl = v-rescale nsttcouple = -1 nh-chain-length = 10 print-nose-hoover-chain-variables = no ; Groups to couple separately tc-grps = system ; Time constant (ps) and reference temperature (K) tau-t= 0.1 ref-t= 323 ; pressure coupling Pcoupl = no Pcoupltype = isotropic nstpcouple = -1 ; Time constant (ps), compressibility (1/bar) and reference P (bar) tau-p= 2.0 compressibility = 4.5e-5 ref-p= 1.0 ; Scaling of reference coordinates, No, All or COM refcoord-scaling = com ; Free energy control stuff free_energy = yes init_lambda_state= 0 delta_lambda = 0 calc_lambda_neighbors= 1; only immediate neighboring windows vdw_lambdas = 0.00 0.00 0.00 0... .70 0.75 0.80 0.85 0.90 0.95 1.00 coul_lambdas = 0.00 0.05 0.10 01.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 ; Options for the decoupling sc-alpha = 0.5 sc-coul = no ; linear interpolation of Coulomb (none in this case) sc-power = 1.0 sc-sigma = 0.3 couple-moltype = Pept ; name of moleculet ype to decouple couple-lambda0 = vdw-q ; only van der Waals interactions couple-lambda1 = none ; turn off everything, in this case only vdW couple-intramol = yes nstdhdl = 10 ; Generate velocities to start gen_vel = yes gen_temp = 300 gen_seed = -1 ; options for bonds constraints = h-bonds ; we only have C-H bonds here ; Type of constraint algorithm constraint-algorithm = lincs ; Do not constrain the starting configuration continuation = no ; Highest order in the expansion of the constraint coupling matrix lincs-order = 12 -- == 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.
