Re: [gmx-users] topology in local?
thank you! On Wed, May 21, 2014 at 4:10 PM, Justin Lemkul jalem...@vt.edu wrote: On 5/21/14, 9:06 AM, Nicola Staffolani wrote: just to improve my knowledge in programming: and I can override it by typing: GMXLIB=address_of_the_new_topology_in_my_computer right? The details depend on your shell. For csh you need setenv, for bash you need export, etc. Quotes shouldn't be necessary, e.g.: export GMXLIB=/home/justin/software/gromacs/custom/share/top But in that case, if I first open a child shell, then the change will be effective only there, and as soon as I come back to the parent shell, GMXLIB will be pointing to the old /usr/share/... address, right? Thank you Justin! Any new shell you open will need the environment variable to be set again; if it's something you need often (or always) set it in .bashrc, .cshrc, etc. -Justin PS I do not think I will try to override it anyway ;) And yes, I manually installed GROMACS because I didn't know I could do it by just using Ubuntu Software Center... On Wed, May 21, 2014 at 2:41 PM, Justin Lemkul jalem...@vt.edu wrote: On 5/21/14, 8:38 AM, Nicola Staffolani wrote: and so how do I make GMXLIB point to somewhere else than /usr/share/gromacs/top? If Gromacs is installed in /usr/share/gromacs, that's where it should point. Otherwise, just override it by setting $GMXLIB in your shell however you like. Hopefully it won't break anything by doing that. -Justin On Wed, May 21, 2014 at 12:58 PM, Chandan Choudhury iitd...@gmail.com wrote: On Wed, May 21, 2014 at 3:57 PM, Nicola Staffolani n.staffol...@unitus.itwrote: Dear Chandan, thank you for your reply. Anyway, before making any change to my GROMACS and therefore risking to destroy, can I ask again your advice? Sure. From what I have read about environment variableshttp://en.wikipedia.org/wiki/Environment_variable#Unix, if another simulation is already running on a computer and I want to launch my simulation but using a different topology, and if my new topology is stored in the directory somewhere/my_topology, then I should send the following command (for example for a md.com command): $GMXLIB=somewhere/my_topology md.com Right? And is it true that the by doing so, I will affect only this simulation, i.e. I will have changed the path to the topology only for this run, while for all the next ones the old path (/usr/share/gromacs/top) will be kept? I do not understand where your confusion lies. BTW, Gromacs works in the following way: 1. pdb2gmx generates the topolopy file (human readable). 2. grompp reads this topology and the structure file to generate a tpr (binary file). In the process of generating the tpr file, it reads the force field (FF) files. The location of the FF is taken from the GMXLIB variable. GMXLIB may point to any path of the computer where the FF is kept. 3. You can use this tpr file, to run your simulation to which every computer you want (gmx should be installed). If a simulation is already running, then your simulation would take more time to complete. Your tpr file will not be affected by the previous simulation. The same is also told by Justin. Thank you, Nicola -- Chandan Kumar Choudhury National Chemical Laboratory, Pune India -- 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 601 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 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users
Re: [gmx-users] How to efficiently fix pbc trajectories problems for VMD using
Dear Dr. Warrem, Dear Tsjerk, Thank you for your emails. Following the suggestion of Dr. Warren I created several dir in which I applied different protocols on my system -- DIR1 -- 1) trjconv_mpi -s npt.tpr -f test.xtc -o test-nojump.xtc -pbc nojump (output System) 2) trjconv_mpi -s npt.tpr -f test-nojump.xtc -o test-center.xtc - center -n iindex.ndx (centering all the frames on Protein) (output system) 3) trjconv_mpi -s npt.tpr -f test-center.xtc -o test-compact.xtc -pbc mol -ur rect (output System) The related Figures are in the following link: http://wikisend.com/download/832038/Figtest1.zip #Comment: I obtain the same result also if a change rect with compact in the third step. -- DIR2 -- 1) trjconv_mpi -s npt.tpr -f test.xtc -o test-nojump.xtc -pbc nojump (output System) 2) trjconv_mpi -s npt.tpr -f test-nojump.xtc -o test-center.xtc - center -n iindex.ndx (centering all the frames on Protein) (output system) 3) trjconv_mpi -s npt.tpr -f test-center.xtc -o test-compact.xtc -pbc mol -ur rect (output System) 4) trjconv_mpi -s npt.tpr -f test-compact.xtc -o test-fit.xtc -fit progressive (fitting on Protein) The pics are here: http://wikisend.com/download/615140/FigTest2.zip #Comment: Here again, I obtain the same results as in the DIR1 but My protein has not translational motions. #Comment: In the step 2 i also centered the system on the Protein_DNA, nothing changes. Then, I tried different pbc/centering combination again but I strongly believe that fixing DNA-Protein complex is enough to obtain a good system. What would do you do to bring back the dsDNA inside the protein? In which step would you operate your command? Thanks in advance for your time. Cheers V Vito Genna, PhD-Fellow Italian Institute of Technology Drug Discovery and Development department Via Morego 30, 16163 Genoa, Italy - The process of scientific discovery is, in effect, a continual flight from wonder. Albert Einstein From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Dallas Warren [dallas.war...@monash.edu] Sent: Thursday, May 22, 2014 1:40 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] How to efficiently fix pbc trajectories problems for VMD using Would suggest that each time you try a different workflow, do so in a new subdirectory and copy the required files into there. That way you ensure are using the files you think that you are. Will help those assisting to then post an image of the coordinate files at each step of the work flow, to see how things are changing, or not. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Vito Genna Sent: Wednesday, 21 May 2014 11:07 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] How to efficiently fix pbc trajectories problems for VMD using Dear Tsjerk, No, it doesn't. (http://wikisend.com/download/324888/Post-nojump.png) I think that the first step need to be changed that's why I tried (whit no success) the flag -pbc whole. I'm still looking for a solution. Thanks again. V Vito Genna, PhD-Fellow Italian Institute of Technology Drug Discovery and Development department Via Morego 30, 16163 Genoa, Italy --- -- The process of scientific discovery is, in effect, a continual flight from wonder. Albert Einstein From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Tsjerk Wassenaar [tsje...@gmail.com] Sent: Wednesday, May 21, 2014 1:48 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] How to efficiently fix pbc trajectories problems for VMD using Hey Vito, After the first step, does the trajectory (say the last frame) look fine? If it does (everything nicely assembled), then after the second step, does it still look fine, and is it placed properly in the center of the box? Cheers, Tsjerk On Wed, May 21, 2014 at 12:50 PM, Vito Genna vito.ge...@iit.it wrote: Hi Tsierk, Ok. 1) trjconv_mpi -s em.tpr -f test.xtc -o test-nojump.xtc -pbc nojump (output System) 2) trjconv_mpi -s em.tpr -f test-nojump.xtc -o test-center.xtc - center -n index.ndx (centering all the frames on different targets
Re: [gmx-users] How to efficiently fix pbc trajectories problems for VMD using
Hi Vito, Does npt.tpr correspond to the first frame of the trajectory and is the structure in npt.tpr correctly assembled? (editconf -f npt.tpr -o npt.tpr.pdb, and check). The only way that -pbc nojump can give a final frame in which the complex is separated is if the reference structure has them already separated. In that case, nothing you'll try will give you what you want. What I do in such cases is dump the first frame, using -pbc whole, and then shift the chains in Pymol according to the box vectors to have them together. Then I use the resulting structure as reference for processing the trajectory. Cheers, Tsjerk On Thu, May 22, 2014 at 10:59 AM, Vito Genna vito.ge...@iit.it wrote: Dear Dr. Warrem, Dear Tsjerk, Thank you for your emails. Following the suggestion of Dr. Warren I created several dir in which I applied different protocols on my system -- DIR1 -- 1) trjconv_mpi -s npt.tpr -f test.xtc -o test-nojump.xtc -pbc nojump (output System) 2) trjconv_mpi -s npt.tpr -f test-nojump.xtc -o test-center.xtc - center -n iindex.ndx (centering all the frames on Protein) (output system) 3) trjconv_mpi -s npt.tpr -f test-center.xtc -o test-compact.xtc -pbc mol -ur rect (output System) The related Figures are in the following link: http://wikisend.com/download/832038/Figtest1.zip #Comment: I obtain the same result also if a change rect with compact in the third step. -- DIR2 -- 1) trjconv_mpi -s npt.tpr -f test.xtc -o test-nojump.xtc -pbc nojump (output System) 2) trjconv_mpi -s npt.tpr -f test-nojump.xtc -o test-center.xtc - center -n iindex.ndx (centering all the frames on Protein) (output system) 3) trjconv_mpi -s npt.tpr -f test-center.xtc -o test-compact.xtc -pbc mol -ur rect (output System) 4) trjconv_mpi -s npt.tpr -f test-compact.xtc -o test-fit.xtc -fit progressive (fitting on Protein) The pics are here: http://wikisend.com/download/615140/FigTest2.zip #Comment: Here again, I obtain the same results as in the DIR1 but My protein has not translational motions. #Comment: In the step 2 i also centered the system on the Protein_DNA, nothing changes. Then, I tried different pbc/centering combination again but I strongly believe that fixing DNA-Protein complex is enough to obtain a good system. What would do you do to bring back the dsDNA inside the protein? In which step would you operate your command? Thanks in advance for your time. Cheers V Vito Genna, PhD-Fellow Italian Institute of Technology Drug Discovery and Development department Via Morego 30, 16163 Genoa, Italy - The process of scientific discovery is, in effect, a continual flight from wonder. Albert Einstein From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [ gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Dallas Warren [dallas.war...@monash.edu] Sent: Thursday, May 22, 2014 1:40 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] How to efficiently fix pbc trajectories problems for VMD using Would suggest that each time you try a different workflow, do so in a new subdirectory and copy the required files into there. That way you ensure are using the files you think that you are. Will help those assisting to then post an image of the coordinate files at each step of the work flow, to see how things are changing, or not. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Vito Genna Sent: Wednesday, 21 May 2014 11:07 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] How to efficiently fix pbc trajectories problems for VMD using Dear Tsjerk, No, it doesn't. (http://wikisend.com/download/324888/Post-nojump.png) I think that the first step need to be changed that's why I tried (whit no success) the flag -pbc whole. I'm still looking for a solution. Thanks again. V Vito Genna, PhD-Fellow Italian Institute of Technology Drug Discovery and Development department Via Morego 30, 16163 Genoa, Italy --- -- The process of scientific discovery is, in effect, a continual flight from wonder. Albert Einstein From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Tsjerk
Re: [gmx-users] How to efficiently fix pbc trajectories problems for VMD using
Dear Tsjerk, I exactly executed: editconf -f npt.tpr -o npt.pdb and I obtained a nicely assembled system (npt.pdb). Well, my system start to cross the boundaries after 20 ns of production phase so the npt.tpr is not the first frame of the trajectories that I trying to fix. After your email I've generated the md_0_1.tpr respecting your request with the command editconf -f md_0_1.tpr -o md_0_1.pdb and again I obtain a well assembled system. The trajectories that I want to fix, is obtained from: trjconv_mpi -f md_0_1.part0001.xtc -o test.xtc -s md_0_1.tpr -skip 100 To be consistent in the procedure, I did again all the steps (-pbc nojump, -center, -compact -ur rect) using the md_0_1.tpr. The result is exactly the same! I'm really losing hope! I will try the Pymol strategy also. Thank you for your hints. Cheers V Vito Genna, PhD-Fellow Italian Institute of Technology Drug Discovery and Development department Via Morego 30, 16163 Genoa, Italy - The process of scientific discovery is, in effect, a continual flight from wonder. Albert Einstein From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Tsjerk Wassenaar [tsje...@gmail.com] Sent: Thursday, May 22, 2014 11:10 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] How to efficiently fix pbc trajectories problems for VMD using Hi Vito, Does npt.tpr correspond to the first frame of the trajectory and is the structure in npt.tpr correctly assembled? (editconf -f npt.tpr -o npt.tpr.pdb, and check). The only way that -pbc nojump can give a final frame in which the complex is separated is if the reference structure has them already separated. In that case, nothing you'll try will give you what you want. What I do in such cases is dump the first frame, using -pbc whole, and then shift the chains in Pymol according to the box vectors to have them together. Then I use the resulting structure as reference for processing the trajectory. Cheers, Tsjerk On Thu, May 22, 2014 at 10:59 AM, Vito Genna vito.ge...@iit.it wrote: Dear Dr. Warrem, Dear Tsjerk, Thank you for your emails. Following the suggestion of Dr. Warren I created several dir in which I applied different protocols on my system -- DIR1 -- 1) trjconv_mpi -s npt.tpr -f test.xtc -o test-nojump.xtc -pbc nojump (output System) 2) trjconv_mpi -s npt.tpr -f test-nojump.xtc -o test-center.xtc - center -n iindex.ndx (centering all the frames on Protein) (output system) 3) trjconv_mpi -s npt.tpr -f test-center.xtc -o test-compact.xtc -pbc mol -ur rect (output System) The related Figures are in the following link: http://wikisend.com/download/832038/Figtest1.zip #Comment: I obtain the same result also if a change rect with compact in the third step. -- DIR2 -- 1) trjconv_mpi -s npt.tpr -f test.xtc -o test-nojump.xtc -pbc nojump (output System) 2) trjconv_mpi -s npt.tpr -f test-nojump.xtc -o test-center.xtc - center -n iindex.ndx (centering all the frames on Protein) (output system) 3) trjconv_mpi -s npt.tpr -f test-center.xtc -o test-compact.xtc -pbc mol -ur rect (output System) 4) trjconv_mpi -s npt.tpr -f test-compact.xtc -o test-fit.xtc -fit progressive (fitting on Protein) The pics are here: http://wikisend.com/download/615140/FigTest2.zip #Comment: Here again, I obtain the same results as in the DIR1 but My protein has not translational motions. #Comment: In the step 2 i also centered the system on the Protein_DNA, nothing changes. Then, I tried different pbc/centering combination again but I strongly believe that fixing DNA-Protein complex is enough to obtain a good system. What would do you do to bring back the dsDNA inside the protein? In which step would you operate your command? Thanks in advance for your time. Cheers V Vito Genna, PhD-Fellow Italian Institute of Technology Drug Discovery and Development department Via Morego 30, 16163 Genoa, Italy - The process of scientific discovery is, in effect, a continual flight from wonder. Albert Einstein From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [ gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Dallas Warren [dallas.war...@monash.edu] Sent: Thursday, May 22, 2014 1:40 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] How to efficiently fix pbc trajectories problems for VMD using Would suggest that each time you try a different workflow, do so in a new subdirectory and copy the required files into there. That way you ensure are using the files you think that you are. Will help those assisting to then post an image of the coordinate
Re: [gmx-users] How to efficiently fix pbc trajectories problems for VMD using
Hey Vito, Don't use -skip. And add -pbc nojump to that first run of trjconv: trjconv_mpi -f md_0_1.part0001.xtc -o test.xtc -s md_0_1.tpr -pbc nojump Then have a look at the last frame to see if it's good. If md_0_1.tpr is assembled properly, then the last frame should be too, provided the assembly did not fall apart (in which case you're in real trouble). Cheers, Tsjerk On Thu, May 22, 2014 at 3:01 PM, Vito Genna vito.ge...@iit.it wrote: Dear Tsjerk, I exactly executed: editconf -f npt.tpr -o npt.pdb and I obtained a nicely assembled system (npt.pdb). Well, my system start to cross the boundaries after 20 ns of production phase so the npt.tpr is not the first frame of the trajectories that I trying to fix. After your email I've generated the md_0_1.tpr respecting your request with the command editconf -f md_0_1.tpr -o md_0_1.pdb and again I obtain a well assembled system. The trajectories that I want to fix, is obtained from: trjconv_mpi -f md_0_1.part0001.xtc -o test.xtc -s md_0_1.tpr -skip 100 To be consistent in the procedure, I did again all the steps (-pbc nojump, -center, -compact -ur rect) using the md_0_1.tpr. The result is exactly the same! I'm really losing hope! I will try the Pymol strategy also. Thank you for your hints. Cheers V Vito Genna, PhD-Fellow Italian Institute of Technology Drug Discovery and Development department Via Morego 30, 16163 Genoa, Italy - The process of scientific discovery is, in effect, a continual flight from wonder. Albert Einstein From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [ gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Tsjerk Wassenaar [tsje...@gmail.com] Sent: Thursday, May 22, 2014 11:10 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] How to efficiently fix pbc trajectories problems for VMD using Hi Vito, Does npt.tpr correspond to the first frame of the trajectory and is the structure in npt.tpr correctly assembled? (editconf -f npt.tpr -o npt.tpr.pdb, and check). The only way that -pbc nojump can give a final frame in which the complex is separated is if the reference structure has them already separated. In that case, nothing you'll try will give you what you want. What I do in such cases is dump the first frame, using -pbc whole, and then shift the chains in Pymol according to the box vectors to have them together. Then I use the resulting structure as reference for processing the trajectory. Cheers, Tsjerk On Thu, May 22, 2014 at 10:59 AM, Vito Genna vito.ge...@iit.it wrote: Dear Dr. Warrem, Dear Tsjerk, Thank you for your emails. Following the suggestion of Dr. Warren I created several dir in which I applied different protocols on my system -- DIR1 -- 1) trjconv_mpi -s npt.tpr -f test.xtc -o test-nojump.xtc -pbc nojump (output System) 2) trjconv_mpi -s npt.tpr -f test-nojump.xtc -o test-center.xtc - center -n iindex.ndx (centering all the frames on Protein) (output system) 3) trjconv_mpi -s npt.tpr -f test-center.xtc -o test-compact.xtc -pbc mol -ur rect (output System) The related Figures are in the following link: http://wikisend.com/download/832038/Figtest1.zip #Comment: I obtain the same result also if a change rect with compact in the third step. -- DIR2 -- 1) trjconv_mpi -s npt.tpr -f test.xtc -o test-nojump.xtc -pbc nojump (output System) 2) trjconv_mpi -s npt.tpr -f test-nojump.xtc -o test-center.xtc - center -n iindex.ndx (centering all the frames on Protein) (output system) 3) trjconv_mpi -s npt.tpr -f test-center.xtc -o test-compact.xtc -pbc mol -ur rect (output System) 4) trjconv_mpi -s npt.tpr -f test-compact.xtc -o test-fit.xtc -fit progressive (fitting on Protein) The pics are here: http://wikisend.com/download/615140/FigTest2.zip #Comment: Here again, I obtain the same results as in the DIR1 but My protein has not translational motions. #Comment: In the step 2 i also centered the system on the Protein_DNA, nothing changes. Then, I tried different pbc/centering combination again but I strongly believe that fixing DNA-Protein complex is enough to obtain a good system. What would do you do to bring back the dsDNA inside the protein? In which step would you operate your command? Thanks in advance for your time. Cheers V Vito Genna, PhD-Fellow Italian Institute of Technology Drug Discovery and Development department Via Morego 30, 16163 Genoa, Italy - The process of scientific discovery is, in effect, a continual flight from wonder. Albert Einstein From:
[gmx-users] Gromacs for reverse transformation
Hello, I want to do a reverse transformation of my system containing: bi-layer, protein and water. The Martini website ( http://md.chem.rug.nl/cgmartini/index.php/reverse-transformation) says to install gromacs version 3.3.1 I am currently using 4.6.1 gromacs version. ques A: Is this version incapable of the transformation? Also, the martini website says to: *1. Unpack the rev_trans.tar.gz in the MARTINITUTORIAL directory that contains all necessary gromacs files for this exercise.* *2. Compile and/or source the modifi ed version of gromacs (remember this tool is based upon gromacs version 3.3.1 and needs the corresponding tricks and threats to be compiled.)* *source /where-ever-you-installed-it/gromacs-3.3.1/bin/GMXRC* ques B:On performing untar on rev_trans.tar.gz there is no MARTINITUTORIAL directory ques C: On performing untar on gmx_rev.tar.gz there is no bin folder KIndly help. Thanks, sxn -- 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] RDF of solvation shell molecules
Hello, I would like to know if it is possible to plot the RDF of water molecules belonging to the solvation shell of a solute. I mean, I want to know the effect of the solute on the water arrangement in the solvation shell. Is there a way to do this? Regards, Sujith. -- 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] 答复: about exchange replica with replicas 140
Did you check the .err file as well? What does it say? How many cores do each node in the HPC have? There might be some issues with the supercomputer that you may be using? One of the nodes might have some issues which is probably causing the problem? I have used 300 cores for replica exchange simulations without any issues. On Thu, May 22, 2014 at 12:47 AM, #ZHANG HAIPING# hzhang...@e.ntu.edu.sgwrote: Dear Justin: The scripts I used is as follow: ## Set job parameters ## Job Name #BSUB -J OpenMPI ## Queue Name #BSUB -q medium_priority ## Output and Input Errors #BSUB -o job%J.out #BSUB -e job%J.err ## Specify walltime in HH:MM #BSUB -W 60:00 ## 16 Processors per Host #BSUB -R span[ptile=16] ## Requesting for 32 cores #BSUB -n 140 # Need to make our own machinefile MACHINEFILE=mymacs.$LSB_JOBID for i in `echo $LSB_HOSTS` do echo $i done $MACHINEFILE ## load module enviroement module load openmpi-1.6.5-intel-v12.1.5 module load intel-12.1.5 ## Run mpi program cd /gpfs/home/hzhang020/REMD/remdrun/scratch /usr/local/RH6_apps/openmpi-1.6.5-intel-v12.1.5/bin/mpirun --bind-to-core --report-bindings -np 140 -machinefile $MACHINEFILE /usr/local/RH6_apps/gromacs-4.6.2-double-intel/bin/mdrun_mpi_d -s prefix_.tpr -multi 140 -replex 3000 There was not obvious error information, just have the output file size is always 0. After long time, I kill it myself. NOTE: The load imbalance in PME FFT and solve is 384%. For optimal PME load balancing PME grid_x (1728) and grid_y (1728) should be divisible by #PME_nodes_x (2) and PME grid_y (1728) and grid_z (1728) should be divisible by #PME_nodes_y (1) NOTE: The load imbalance in PME FFT and solve is 384%. For optimal PME load balancing PME grid_x (1728) and grid_y (1728) should be divisible by #PME_nodes_x (2) and PME grid_y (1728) and grid_z (1728) should be divisible by #PME_nodes_y (1) -- WARNING: A process refused to die! Host: comp094 PID: 6751 This process may still be running and/or consuming resources. -- -- mpirun noticed that process rank 273 with PID 30914 on node comp122 exited on signal 9 (Killed). -- 发件人: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se 代表 Justin Lemkul jalem...@vt.edu 发送时间: 2014年5月22日 10:57 收件人: gmx-us...@gromacs.org 主题: Re: [gmx-users] about exchange replica with replicas 140 On 5/21/14, 10:53 PM, #ZHANG HAIPING# wrote: Dear gromacs user: I have encounter a problem when used HPC(high performance computer) to run replica exchange. I find that when I used replica over 128, it will not work, while under 128 , it is ok, even when I used cores much more than 128(several cores for one replica). The version I used is gromacs-4.6.2-double-intel. Hope for you help. You need to provide more information. Specifically, what commands are you issuing? What does will not work mean? Is there a specific error you are getting? -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 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.
Re: [gmx-users] Nanoparticle topology
Parameters for metals are readily available in various forcefields in Gromacs. If your nanoparticles are gold spheres suspended freely in the system, then you can just get the parameters from from the forcefield files and specify the number of gold atoms in the topology file. On Wed, May 21, 2014 at 9:34 PM, guhansingh guhansi...@gmail.com wrote: Dear sir, I need to simulate gold nanoparticles (*NP*) interaction with some ligands (drugs). I can get ligand topology via ATB/ Prodrug server, but I can't get nanoparticle topology. Is there any external tools for *NP* modelling and topology generation.? Any other modifications to simulate metal atoms via GROMACS.? Thanks in advance -- Guhan.KA -- 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] (no subject)
You should provide with more information. The error message clearly states that there are multiple definitions for the moleculetype CU1. You should check carefully for redundancies in the top file On Wed, May 21, 2014 at 2:57 AM, Meenakshi Rajput ashi.rajpu...@gmail.comwrote: dear gromacs users I tried to add ions to my .gro file as it was showing the warning that:- System has non zero charge. But a new error occured when i run grompp command again:- Program grompp_d, VERSION 4.6.3 Source code file: /build/buildd/gromacs-4.6.3/src/kernel/toppush.c, line: 1412 Fatal error: moleculetype CU1 is redefined For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Please help me... -- 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 for reverse transformation
Hi sxn, I would argue that that method for reverse transformation is largely obsolete. Please have a look at http://www.cgmartini.nl/cgmartini/index.php/back Cheers, Tsjerk On Thu, May 22, 2014 at 4:26 PM, shivangi nangia shivangi.nan...@gmail.comwrote: Hello, I want to do a reverse transformation of my system containing: bi-layer, protein and water. The Martini website ( http://md.chem.rug.nl/cgmartini/index.php/reverse-transformation) says to install gromacs version 3.3.1 I am currently using 4.6.1 gromacs version. ques A: Is this version incapable of the transformation? Also, the martini website says to: *1. Unpack the rev_trans.tar.gz in the MARTINITUTORIAL directory that contains all necessary gromacs files for this exercise.* *2. Compile and/or source the modifi ed version of gromacs (remember this tool is based upon gromacs version 3.3.1 and needs the corresponding tricks and threats to be compiled.)* *source /where-ever-you-installed-it/gromacs-3.3.1/bin/GMXRC* ques B:On performing untar on rev_trans.tar.gz there is no MARTINITUTORIAL directory ques C: On performing untar on gmx_rev.tar.gz there is no bin folder KIndly help. Thanks, sxn -- 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. -- Tsjerk A. Wassenaar, Ph.D. -- 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 efficiently fix pbc trajectories problems for VMD using
Dear Tsjerk, I'm glad to write to you because it works fine! The system is now perfectly assemble. -pbc nojump using the md_0_1.tpr is enough to rebuild the system. The only problem is the water that diffuses leaving the protein. I think that with the -center flag i can bring back H20 inside the box. Thank you so much! I was doing a lot of attempts! Cheers Vito Vito Genna, PhD-Fellow Italian Institute of Technology Drug Discovery and Development department Via Morego 30, 16163 Genoa, Italy - The process of scientific discovery is, in effect, a continual flight from wonder. Albert Einstein From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Tsjerk Wassenaar [tsje...@gmail.com] Sent: Thursday, May 22, 2014 4:06 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] How to efficiently fix pbc trajectories problems for VMD using Hey Vito, Don't use -skip. And add -pbc nojump to that first run of trjconv: trjconv_mpi -f md_0_1.part0001.xtc -o test.xtc -s md_0_1.tpr -pbc nojump Then have a look at the last frame to see if it's good. If md_0_1.tpr is assembled properly, then the last frame should be too, provided the assembly did not fall apart (in which case you're in real trouble). Cheers, Tsjerk On Thu, May 22, 2014 at 3:01 PM, Vito Genna vito.ge...@iit.it wrote: Dear Tsjerk, I exactly executed: editconf -f npt.tpr -o npt.pdb and I obtained a nicely assembled system (npt.pdb). Well, my system start to cross the boundaries after 20 ns of production phase so the npt.tpr is not the first frame of the trajectories that I trying to fix. After your email I've generated the md_0_1.tpr respecting your request with the command editconf -f md_0_1.tpr -o md_0_1.pdb and again I obtain a well assembled system. The trajectories that I want to fix, is obtained from: trjconv_mpi -f md_0_1.part0001.xtc -o test.xtc -s md_0_1.tpr -skip 100 To be consistent in the procedure, I did again all the steps (-pbc nojump, -center, -compact -ur rect) using the md_0_1.tpr. The result is exactly the same! I'm really losing hope! I will try the Pymol strategy also. Thank you for your hints. Cheers V Vito Genna, PhD-Fellow Italian Institute of Technology Drug Discovery and Development department Via Morego 30, 16163 Genoa, Italy - The process of scientific discovery is, in effect, a continual flight from wonder. Albert Einstein From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [ gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Tsjerk Wassenaar [tsje...@gmail.com] Sent: Thursday, May 22, 2014 11:10 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] How to efficiently fix pbc trajectories problems for VMD using Hi Vito, Does npt.tpr correspond to the first frame of the trajectory and is the structure in npt.tpr correctly assembled? (editconf -f npt.tpr -o npt.tpr.pdb, and check). The only way that -pbc nojump can give a final frame in which the complex is separated is if the reference structure has them already separated. In that case, nothing you'll try will give you what you want. What I do in such cases is dump the first frame, using -pbc whole, and then shift the chains in Pymol according to the box vectors to have them together. Then I use the resulting structure as reference for processing the trajectory. Cheers, Tsjerk On Thu, May 22, 2014 at 10:59 AM, Vito Genna vito.ge...@iit.it wrote: Dear Dr. Warrem, Dear Tsjerk, Thank you for your emails. Following the suggestion of Dr. Warren I created several dir in which I applied different protocols on my system -- DIR1 -- 1) trjconv_mpi -s npt.tpr -f test.xtc -o test-nojump.xtc -pbc nojump (output System) 2) trjconv_mpi -s npt.tpr -f test-nojump.xtc -o test-center.xtc - center -n iindex.ndx (centering all the frames on Protein) (output system) 3) trjconv_mpi -s npt.tpr -f test-center.xtc -o test-compact.xtc -pbc mol -ur rect (output System) The related Figures are in the following link: http://wikisend.com/download/832038/Figtest1.zip #Comment: I obtain the same result also if a change rect with compact in the third step. -- DIR2 -- 1) trjconv_mpi -s npt.tpr -f test.xtc -o test-nojump.xtc -pbc nojump (output System) 2) trjconv_mpi -s npt.tpr -f test-nojump.xtc -o test-center.xtc - center -n iindex.ndx (centering all the frames on Protein) (output system) 3) trjconv_mpi -s npt.tpr -f test-center.xtc -o test-compact.xtc -pbc mol -ur rect (output System) 4) trjconv_mpi -s npt.tpr -f test-compact.xtc -o
Re: [gmx-users] Multi-node GPU runs crashing with a fork() warning
Hey, Yes, everything runs fine if I work on one node with one or more GPU's. The crash occurs, similar to the previous mailing list post: http://comments.gmane.org/gmane.science.biology.gromacs.user/63911 It crashes when we attempt to work across multiple GPU enabled nodes. This happens when our cluster of C2050's is used but not when our nodes with K20's are used. The CPU architecture on the two node types are also slightly different but both are Intel hardware. Hopefully there is a solution. Thanks for the tips on launch configurations. I think my simulations are scaling pretty well with the GPU's. I'm working with a dense city of many millions of atoms. On Wed, May 21, 2014 at 8:52 PM, Szilárd Páll pall.szil...@gmail.comwrote: Hi, Sounds like an MPI or MPI+CUDA issue. Does mdrun run if you use a single GPU? How about two? Btw, unless you have some rather exotic setup, you won't be able to get much improvement from using more than three, at most four GPUs per node - you need CPU cores to match them (and a large system to deed the GPUs and scale). Multi runs could work well, though. Cheers, -- Szilárd On Wed, May 21, 2014 at 6:29 PM, Thomas C. O'Connor tocon...@jhu.edu wrote: Hey Folks, I'm attempting to run simulations on a multi-node gpu cluster and my simulations are crashing after flagging a open-mpi fork() warning: *--* *An MPI process has executed an operation involving a call to the* *fork() system call to create a child process. Open MPI is currently* *operating in a condition that could result in memory corruption or* *other system errors; your MPI job may hang, crash, or produce silent* *data corruption. The use of fork() (or system() or other calls that* *create child processes) is strongly discouraged.* *The process that invoked fork was:* * Local host: lngpu019 (PID 11549)* * MPI_COMM_WORLD rank: 18* *If you are *absolutely sure* that your application will successfully* *and correctly survive a call to fork(), you may disable this warning* *by setting the mpi_warn_on_fork MCA parameter to 0.* *--* I saw a similar mailing-list post about this sort of issue from September 2013, but the thread had no resolution. - Each node of our cluster has has 12 intel cores and 6 NVIDIA Tesla C2050 GPU's. - we call: mpirun -machinefile nodes.txt -npernode 6 mdrun_mpi - I compiled GROMACS on one of the compute nodes with the C2050's. We also have a few nodes with newer K20 NVIDIA GPU's. When we compile GROMACS on these nodes we can run the code across multiple nodes and GPU's without any errors. I don't know if the fork() error is directly related to the crash or not; or if there might be obscure, device specific object files outside my build directory, that I should delete. Any insight you folks could provide to help me solve this issue would be appreciated. Thanks, -- Thomas O'Connor Graduate Research Assistant MCS IGERT Fellow Department of Physics Astronomy The Johns Hopkins University 3701 San Martin Drive Baltimore, MD 21218*tocon...@jhu.edu tocon...@jhu.edu*410.516.8587 -- 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. -- Thomas O'Connor Graduate Research Assistant MCS IGERT Fellow Department of Physics Astronomy The Johns Hopkins University 3701 San Martin Drive Baltimore, MD 21218*tocon...@jhu.edu tocon...@jhu.edu*410.516.8587 -- 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] BCAM Internship Position Announcement
The following BCAM Internship position is open at BCAM – Basque Center for Applied Mathematics, an interdisciplinary research center located in Bilbao. The interested applicants can apply via the following webpage: http://www.bcamath.org/en/research/internships INTERNSHIP DATA Research topic title: Free energy calculations using molecular dynamics and Markov chain Monte Carlo methods Research topic description: Study, implementation and testing of Monte Carlo techniques combined with classical molecular dynamics (MD) with the ultimate objective of calculating protein binding energies ΔG. The project will result in a new simulation method based on the adaptation of the existing Generalized Shadow Hybrid Monte Carlo (GSHMC) to umbrella sampling. The tasks to be performed by the intern involve: - modifying the open-source software MD package GROMACS - setting up and running simulations of biomolecular systems using the modified software on parallel computational servers - analysing results and calculating ΔG using the potential of mean force curve Keywords: Molecular Dynamics, Hybrid Monte Carlo, Umbrella sampling, Hamiltonian dynamics Required knowledge and skills: Hamiltonian dynamics, Monte Carlo sampling, C programming, Unix/Linux Required language skills: English Duration and dates: 2-3 months during 2014 Application deadline: June 1st, 2014 Supervisor: Bruno Escribano and Elena Akhmatskaya Research line: Modelling and Simulation in Life and Materials Sciences - M3A Research Area --- Bruno Escribano BCAM Researcher BCAM – Basque Center for Applied Mathematics Alameda de Mazarredo, 14 E-48009 Bilbao - Basque Country - Spain Tel. +34 946 567 853 bescrib...@bcamath.org | www.bcamath.org ( matematika mugaz bestalde ) -- 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] RDF of solvation shell molecules
Hi Sujith, g_rdf is the tool you need. Chandan On Thu, May 22, 2014 at 8:18 PM, sujithkakkat . sujithk...@gmail.comwrote: Hello, I would like to know if it is possible to plot the RDF of water molecules belonging to the solvation shell of a solute. I mean, I want to know the effect of the solute on the water arrangement in the solvation shell. Is there a way to do this? Regards, Sujith. -- 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. -- -- Chandan Kumar Choudhury National Chemical Laboratory, Pune India -- 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] Multi-node GPU runs crashing with a fork() warning
On Thu, May 22, 2014 at 5:31 PM, Thomas C. O'Connor tocon...@jhu.eduwrote: Hey, Yes, everything runs fine if I work on one node with one or more GPU's. The crash occurs, similar to the previous mailing list post: http://comments.gmane.org/gmane.science.biology.gromacs.user/63911 It crashes when we attempt to work across multiple GPU enabled nodes. This happens when our cluster of C2050's is used but not when our nodes with K20's are used. The CPU architecture on the two node types are also slightly different but both are Intel hardware. I would suspect a difference in CUDA version, CUDA driver version, or MPI version could be the origin here (see top of mdrun log file for some information here). Normal use of mdrun does not use system() or fork() or make child processes, which is the basis for my suspicion that the problem is not within GROMACS. If there's a way to run some other MPI+GPU code on the machine, whether it works might be useful information. Running mdrun within a debugger will permit you to observe whether the crash is before mdrun starts, or not. Hopefully there is a solution. Thanks for the tips on launch configurations. I think my simulations are scaling pretty well with the GPU's. I'm working with a dense city of many millions of atoms. Good, you'd want to be doing something like that. Mark On Wed, May 21, 2014 at 8:52 PM, Szilárd Páll pall.szil...@gmail.com wrote: Hi, Sounds like an MPI or MPI+CUDA issue. Does mdrun run if you use a single GPU? How about two? Btw, unless you have some rather exotic setup, you won't be able to get much improvement from using more than three, at most four GPUs per node - you need CPU cores to match them (and a large system to deed the GPUs and scale). Multi runs could work well, though. Cheers, -- Szilárd On Wed, May 21, 2014 at 6:29 PM, Thomas C. O'Connor tocon...@jhu.edu wrote: Hey Folks, I'm attempting to run simulations on a multi-node gpu cluster and my simulations are crashing after flagging a open-mpi fork() warning: *--* *An MPI process has executed an operation involving a call to the* *fork() system call to create a child process. Open MPI is currently* *operating in a condition that could result in memory corruption or* *other system errors; your MPI job may hang, crash, or produce silent* *data corruption. The use of fork() (or system() or other calls that* *create child processes) is strongly discouraged.* *The process that invoked fork was:* * Local host: lngpu019 (PID 11549)* * MPI_COMM_WORLD rank: 18* *If you are *absolutely sure* that your application will successfully* *and correctly survive a call to fork(), you may disable this warning* *by setting the mpi_warn_on_fork MCA parameter to 0.* *--* I saw a similar mailing-list post about this sort of issue from September 2013, but the thread had no resolution. - Each node of our cluster has has 12 intel cores and 6 NVIDIA Tesla C2050 GPU's. - we call: mpirun -machinefile nodes.txt -npernode 6 mdrun_mpi - I compiled GROMACS on one of the compute nodes with the C2050's. We also have a few nodes with newer K20 NVIDIA GPU's. When we compile GROMACS on these nodes we can run the code across multiple nodes and GPU's without any errors. I don't know if the fork() error is directly related to the crash or not; or if there might be obscure, device specific object files outside my build directory, that I should delete. Any insight you folks could provide to help me solve this issue would be appreciated. Thanks, -- Thomas O'Connor Graduate Research Assistant MCS IGERT Fellow Department of Physics Astronomy The Johns Hopkins University 3701 San Martin Drive Baltimore, MD 21218*tocon...@jhu.edu tocon...@jhu.edu*410.516.8587 -- 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. -- Thomas O'Connor Graduate Research Assistant MCS IGERT Fellow Department
Re: [gmx-users] Gromacs for reverse transformation
Hi Tsjerk, Do the scripts available in the backward.zip file http://www.cgmartini.nl/cgmartini/images/tools/backward/backward.zip help me to backmap a coarse-grained polymer? Chandan On Thu, May 22, 2014 at 8:31 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi sxn, I would argue that that method for reverse transformation is largely obsolete. Please have a look at http://www.cgmartini.nl/cgmartini/index.php/back Cheers, Tsjerk On Thu, May 22, 2014 at 4:26 PM, shivangi nangia shivangi.nan...@gmail.comwrote: Hello, I want to do a reverse transformation of my system containing: bi-layer, protein and water. The Martini website ( http://md.chem.rug.nl/cgmartini/index.php/reverse-transformation) says to install gromacs version 3.3.1 I am currently using 4.6.1 gromacs version. ques A: Is this version incapable of the transformation? Also, the martini website says to: *1. Unpack the rev_trans.tar.gz in the MARTINITUTORIAL directory that contains all necessary gromacs files for this exercise.* *2. Compile and/or source the modifi ed version of gromacs (remember this tool is based upon gromacs version 3.3.1 and needs the corresponding tricks and threats to be compiled.)* *source /where-ever-you-installed-it/gromacs-3.3.1/bin/GMXRC* ques B:On performing untar on rev_trans.tar.gz there is no MARTINITUTORIAL directory ques C: On performing untar on gmx_rev.tar.gz there is no bin folder KIndly help. Thanks, sxn -- 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. -- Tsjerk A. Wassenaar, Ph.D. -- 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. -- -- Chandan Kumar Choudhury National Chemical Laboratory, Pune India -- 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 for reverse transformation
Hi Chandan, You may have to write a mapping file, as explained in one of the tutorials in the supplementary information of the paper. If that poses problems, you can contact me. I may be interested in adding new mappings :) Cheers, Tsjerk On May 22, 2014 6:42 PM, Chandan Choudhury iitd...@gmail.com wrote: Hi Tsjerk, Do the scripts available in the backward.zip file http://www.cgmartini.nl/cgmartini/images/tools/backward/backward.zip help me to backmap a coarse-grained polymer? Chandan On Thu, May 22, 2014 at 8:31 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi sxn, I would argue that that method for reverse transformation is largely obsolete. Please have a look at http://www.cgmartini.nl/cgmartini/index.php/back Cheers, Tsjerk On Thu, May 22, 2014 at 4:26 PM, shivangi nangia shivangi.nan...@gmail.comwrote: Hello, I want to do a reverse transformation of my system containing: bi-layer, protein and water. The Martini website ( http://md.chem.rug.nl/cgmartini/index.php/reverse-transformation) says to install gromacs version 3.3.1 I am currently using 4.6.1 gromacs version. ques A: Is this version incapable of the transformation? Also, the martini website says to: *1. Unpack the rev_trans.tar.gz in the MARTINITUTORIAL directory that contains all necessary gromacs files for this exercise.* *2. Compile and/or source the modifi ed version of gromacs (remember this tool is based upon gromacs version 3.3.1 and needs the corresponding tricks and threats to be compiled.)* *source /where-ever-you-installed-it/gromacs-3.3.1/bin/GMXRC* ques B:On performing untar on rev_trans.tar.gz there is no MARTINITUTORIAL directory ques C: On performing untar on gmx_rev.tar.gz there is no bin folder KIndly help. Thanks, sxn -- 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. -- Tsjerk A. Wassenaar, Ph.D. -- 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. -- -- Chandan Kumar Choudhury National Chemical Laboratory, Pune India -- 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 for reverse transformation
Thanks a lot Tsjerk. Thanks, Shivangi Nangia, Ph. D Postdoctoral Research Associate Department of Molecular and Cell Biology University of Connecticut On Thu, May 22, 2014 at 11:01 AM, Tsjerk Wassenaar tsje...@gmail.comwrote: Hi sxn, I would argue that that method for reverse transformation is largely obsolete. Please have a look at http://www.cgmartini.nl/cgmartini/index.php/back Cheers, Tsjerk On Thu, May 22, 2014 at 4:26 PM, shivangi nangia shivangi.nan...@gmail.comwrote: Hello, I want to do a reverse transformation of my system containing: bi-layer, protein and water. The Martini website ( http://md.chem.rug.nl/cgmartini/index.php/reverse-transformation) says to install gromacs version 3.3.1 I am currently using 4.6.1 gromacs version. ques A: Is this version incapable of the transformation? Also, the martini website says to: *1. Unpack the rev_trans.tar.gz in the MARTINITUTORIAL directory that contains all necessary gromacs files for this exercise.* *2. Compile and/or source the modifi ed version of gromacs (remember this tool is based upon gromacs version 3.3.1 and needs the corresponding tricks and threats to be compiled.)* *source /where-ever-you-installed-it/gromacs-3.3.1/bin/GMXRC* ques B:On performing untar on rev_trans.tar.gz there is no MARTINITUTORIAL directory ques C: On performing untar on gmx_rev.tar.gz there is no bin folder KIndly help. Thanks, sxn -- 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. -- Tsjerk A. Wassenaar, Ph.D. -- 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 for reverse transformation
Hello Tsjerk, Is there any example/tutorial on how to use the backward apart from the notes in the initram.sh Thanks, sxn On Thu, May 22, 2014 at 1:41 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Chandan, You may have to write a mapping file, as explained in one of the tutorials in the supplementary information of the paper. If that poses problems, you can contact me. I may be interested in adding new mappings :) Cheers, Tsjerk On May 22, 2014 6:42 PM, Chandan Choudhury iitd...@gmail.com wrote: Hi Tsjerk, Do the scripts available in the backward.zip file http://www.cgmartini.nl/cgmartini/images/tools/backward/backward.ziphelp me to backmap a coarse-grained polymer? Chandan On Thu, May 22, 2014 at 8:31 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi sxn, I would argue that that method for reverse transformation is largely obsolete. Please have a look at http://www.cgmartini.nl/cgmartini/index.php/back Cheers, Tsjerk On Thu, May 22, 2014 at 4:26 PM, shivangi nangia shivangi.nan...@gmail.comwrote: Hello, I want to do a reverse transformation of my system containing: bi-layer, protein and water. The Martini website ( http://md.chem.rug.nl/cgmartini/index.php/reverse-transformation) says to install gromacs version 3.3.1 I am currently using 4.6.1 gromacs version. ques A: Is this version incapable of the transformation? Also, the martini website says to: *1. Unpack the rev_trans.tar.gz in the MARTINITUTORIAL directory that contains all necessary gromacs files for this exercise.* *2. Compile and/or source the modifi ed version of gromacs (remember this tool is based upon gromacs version 3.3.1 and needs the corresponding tricks and threats to be compiled.)* *source /where-ever-you-installed-it/gromacs-3.3.1/bin/GMXRC* ques B:On performing untar on rev_trans.tar.gz there is no MARTINITUTORIAL directory ques C: On performing untar on gmx_rev.tar.gz there is no bin folder KIndly help. Thanks, sxn -- 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-usersor send a mail to gmx-users-requ...@gromacs.org. -- Tsjerk A. Wassenaar, Ph.D. -- 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. -- -- Chandan Kumar Choudhury National Chemical Laboratory, Pune India -- 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] Odd protein behavior in MD
I ran a 8 ns simulation on a small protein in a water box using PBC. I then calculated the RMS using g_rms command. When I plotted the outcome my rms graph looked like a Histogram instead of a rms plot. I then took a region of the trajectories and view them in VMD. The protein starts out ok, but suddenly blows up in the since that separate parts of the protein went to the four corners of the box...I thought maybe this was a problem of PBC where parts of my protein were leaving the box and so, I attempted to center protein and water back into the center of the box using the following procedure: trjconv -s pr.tpr -f pr1_13.xtc -center -o file.xtc However, this did not correct the problem...Can someone please inform as to what the problem is??? The total energy and potential energy looks ok and so, I am lost as to what is happening or how to fix it. 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.
Re: [gmx-users] Gromacs for reverse transformation
Hi sxn, The paper describing the method has a tutorial as supplementary material. It's also available from our site at the University of Erlangen, but I'l have to look up the address. In addition, Alex de Vries from Groningen recently developed another tutorial for a hands-on session he arranged. Not sure if it is available online, I'll ask him to seenif we can add it to the backward site at cgmartini.nl. Cheers, Tsjerk On May 22, 2014 9:28 PM, shivangi nangia shivangi.nan...@gmail.com wrote: Hello Tsjerk, Is there any example/tutorial on how to use the backward apart from the notes in the initram.sh Thanks, sxn On Thu, May 22, 2014 at 1:41 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Chandan, You may have to write a mapping file, as explained in one of the tutorials in the supplementary information of the paper. If that poses problems, you can contact me. I may be interested in adding new mappings :) Cheers, Tsjerk On May 22, 2014 6:42 PM, Chandan Choudhury iitd...@gmail.com wrote: Hi Tsjerk, Do the scripts available in the backward.zip file http://www.cgmartini.nl/cgmartini/images/tools/backward/backward.ziphelp me to backmap a coarse-grained polymer? Chandan On Thu, May 22, 2014 at 8:31 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi sxn, I would argue that that method for reverse transformation is largely obsolete. Please have a look at http://www.cgmartini.nl/cgmartini/index.php/back Cheers, Tsjerk On Thu, May 22, 2014 at 4:26 PM, shivangi nangia shivangi.nan...@gmail.comwrote: Hello, I want to do a reverse transformation of my system containing: bi-layer, protein and water. The Martini website ( http://md.chem.rug.nl/cgmartini/index.php/reverse-transformation) says to install gromacs version 3.3.1 I am currently using 4.6.1 gromacs version. ques A: Is this version incapable of the transformation? Also, the martini website says to: *1. Unpack the rev_trans.tar.gz in the MARTINITUTORIAL directory that contains all necessary gromacs files for this exercise.* *2. Compile and/or source the modifi ed version of gromacs (remember this tool is based upon gromacs version 3.3.1 and needs the corresponding tricks and threats to be compiled.)* *source /where-ever-you-installed-it/gromacs-3.3.1/bin/GMXRC* ques B:On performing untar on rev_trans.tar.gz there is no MARTINITUTORIAL directory ques C: On performing untar on gmx_rev.tar.gz there is no bin folder KIndly help. Thanks, sxn -- 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-usersor send a mail to gmx-users-requ...@gromacs.org. -- Tsjerk A. Wassenaar, Ph.D. -- 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-usersor send a mail to gmx-users-requ...@gromacs.org. -- -- Chandan Kumar Choudhury National Chemical Laboratory, Pune India -- 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
Re: [gmx-users] Odd protein behavior in MD
Hi, The usual workflow to fix these kinds of pbc issues can be found here: http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions Mark On Thu, May 22, 2014 at 9:48 PM, Steve Seibold steve...@ymail.com wrote: I ran a 8 ns simulation on a small protein in a water box using PBC. I then calculated the RMS using g_rms command. When I plotted the outcome my rms graph looked like a Histogram instead of a rms plot. I then took a region of the trajectories and view them in VMD. The protein starts out ok, but suddenly blows up in the since that separate parts of the protein went to the four corners of the box...I thought maybe this was a problem of PBC where parts of my protein were leaving the box and so, I attempted to center protein and water back into the center of the box using the following procedure: trjconv -s pr.tpr -f pr1_13.xtc -center -o file.xtc However, this did not correct the problem...Can someone please inform as to what the problem is??? The total energy and potential energy looks ok and so, I am lost as to what is happening or how to fix it. 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. -- 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] g_disre problem
I'm trying to use g_disre to analyze NOE-derived distance restraints in my simulation as : g_disre -s gromacs46-run20.tpr -f run-20-dt100-nojump.pdb And I get the error (logfile attached) : Program g_disre, VERSION 4.6.5 Source code file: /root/gromacs-4.6.5/src/tools/gmx_disre.c, line: 189 Fatal error: tpr inconsistency. ndr = 728, label = 0 Now there are 728 distance restraints, indexed from 0 to 727 in the itp file and they are read correctly (from log file: There are 4646 distance restraints involving 4646 atom pairs, there is more than one pair in each restraint). So I don’t know how to fix this now. Thanks in advance for any help, Harish -- 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] from amber to opls
Hi, I have done a simulation of an organic molecule (a cyclodextrin) using GAFF/AMBER parameters, and I would like to compare the results using another force-field (OPLS or CHARMM). Is there any direct way to go from the topology for AMBER to the topology for OPLS or CHARMM? Thanks a lot for your help in advance. Best wishes, Rebeca. Dr. Rebeca Garcia Santiago de Compostela University Spain -- 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] from amber to opls
On 5/22/14, 5:19 PM, Rebeca García Fandiño wrote: Hi, I have done a simulation of an organic molecule (a cyclodextrin) using GAFF/AMBER parameters, and I would like to compare the results using another force-field (OPLS or CHARMM). Is there any direct way to go from the topology for AMBER to the topology for OPLS or CHARMM? You can't simply translate one force field to another. You need to derive a new topology that is consistent with the other force field. For CHARMM, you can use the ParamChem server to derive parameters under CGenFF; the output topologies are generally very high quality, though some small empirical adjustments may be necessary, but the majority of the hard work is already done :) -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 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] mdrun_mpi with cmake
Hi, I would like to generate specifically mdrun with mpi support. with configure/make it was possible to use configure ... make mdrun make install mdrun How would you do this with cmake? best regards Soren -- 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] mdrun_mpi with cmake
http://www.gromacs.org/Documentation/Installation_Instructions#4.2._Using_CMake_command-line_options With 4.5/6 we generate a target with CMake called install-mdrun, so make install-mdrun will work. With 5.0 things will change a bit and you'll have to turn on an mdrun-only build. -- Szilárd On Fri, May 23, 2014 at 12:16 AM, Soren Wacker swac...@ucalgary.ca wrote: Hi, I would like to generate specifically mdrun with mpi support. with configure/make it was possible to use configure ... make mdrun make install mdrun How would you do this with cmake? best regards Soren -- 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] mdrun_mpi with cmake
Thanks! That means you compile everything with cmake make #and only at the last step the build is limited to mdrun? make-mdrun Do you already know how you will turn on an 'mdrun-only build' ? best Soren -- 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] mdrun_mpi with cmake with GMX_BUILD_MDRUN_ONLY=ON
Ok, actually, both solutions generated mdrun_mpi. Would you recommend to set a suffix for the libraries as well? @Justin: I've got Manually-specified variables were not used by the project: GMX_BUILD_MDRUN_ONLY Does this mean the variable is not used at all, or just not here? Or should I set it as environment variable??? Is this the solution for gromacs 5? I am compiling 4.6.5. cmake command was: cmake .. -DFFTWF_INCLUDE_DIR=/home/swacker/Programme/fftw3/single/include -DFFTWF_LIBRARY=~/Programme/fftw3/single/lib/libfftw3f.a -DCMAKE_INSTALL_PREFIX=~/Programme/gromacs/gromacs-4.6.5-gcc-fftw3-single -DGMX_MPI=ON -DGMX_BINARY_SUFFIX=_mpi -DGMX_DEFAULT_SUFFIX=OFF -DGMX_BUILD_MDRUN_ONLY=ON From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Justin Lemkul [jalem...@vt.edu] Sent: Thursday, May 22, 2014 4:38 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] mdrun_mpi with cmake On 5/22/14, 6:36 PM, Soren Wacker wrote: Thanks! That means you compile everything with cmake make #and only at the last step the build is limited to mdrun? make-mdrun Do you already know how you will turn on an 'mdrun-only build' ? No, use cmake -DGMX_BUILD_MDRUN_ONLY=ON -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 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] mdrun_mpi with cmake with GMX_BUILD_MDRUN_ONLY=ON
On 5/22/14, 6:57 PM, Soren Wacker wrote: Ok, actually, both solutions generated mdrun_mpi. Would you recommend to set a suffix for the libraries as well? @Justin: I've got Manually-specified variables were not used by the project: GMX_BUILD_MDRUN_ONLY Does this mean the variable is not used at all, or just not here? Or should I set it as environment variable??? Is this the solution for gromacs 5? Yes, that is for 5.0. -Justin I am compiling 4.6.5. cmake command was: cmake .. -DFFTWF_INCLUDE_DIR=/home/swacker/Programme/fftw3/single/include -DFFTWF_LIBRARY=~/Programme/fftw3/single/lib/libfftw3f.a -DCMAKE_INSTALL_PREFIX=~/Programme/gromacs/gromacs-4.6.5-gcc-fftw3-single -DGMX_MPI=ON -DGMX_BINARY_SUFFIX=_mpi -DGMX_DEFAULT_SUFFIX=OFF -DGMX_BUILD_MDRUN_ONLY=ON From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Justin Lemkul [jalem...@vt.edu] Sent: Thursday, May 22, 2014 4:38 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] mdrun_mpi with cmake On 5/22/14, 6:36 PM, Soren Wacker wrote: Thanks! That means you compile everything with cmake make #and only at the last step the build is limited to mdrun? make-mdrun Do you already know how you will turn on an 'mdrun-only build' ? No, use cmake -DGMX_BUILD_MDRUN_ONLY=ON -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 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 601 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] mdrun_mpi with cmake with GMX_BUILD_MDRUN_ONLY=ON
...and apparently everything gets compiled. -- 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] mdrun_mpi with cmake with GMX_BUILD_MDRUN_ONLY=ON
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.
[gmx-users] counter ions in coarse grained simulations
Hi List, My query is not really related to gromacs but I appreciate response from people who might have tried using coarse grained simualtions using Martini force field in gromacs. I haven't come across tutorial or mailing list where people have added counter ions to a coarse grained protein system. Do we also coarse grained counter-ions ? or Do I assume that some sort of potential will take care of the effect? Or are the parameters from atomistic force fields are retained for counter-ions? How do I add counter-ions in gromacs to coarse grained topology? Your feedback is appreciated. Regards, Neha -- 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] rhombic dodecahedron construction
Hi, I'm trying to figure out how to construct a rhombic dodecahedron for a membrane system. The manual (Section 3.2.1) states: There are two different orientations of a rhombic dodecahedron that satisfy equations 3.1, 3.2 and 3.3. The program editconf produces the orientation which has a square intersection with the xy-plane. This orientation was chosen because the first two box vectors coincide with the x and y-axis, which is easier to comprehend. The other orientation can be useful for simulations of membrane proteins. In this case the cross-section with the xy-plane is a hexagon, which has an area which is 14% smaller than the area of a square with the same image distance. The height of the box (cz) should be changed to obtain an optimal spacing. I can't figure out how to construct the system with a hexagon on the x-y plane, I presume I can rotate the box but I can only visualise the result as a triclinic cell. I also can't figure out how to adjust the height of the box, editconf only accepts a single magnitude for dodecahedron vector lengths. Any help would be greatly appreciated. Thanks in advance, -Trayder -- 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] RDF of solvation shell molecules
Hello Chandan, Thank you for the response. I have used g_rdf, but I guess it gives the RDF for the whole system. Say, if I choose water oxygen, it will plot RDF from water molecules in the whole system. But, I want the RDF for the solvation shell water molecules ,leaving the bulk water . I came across such a plot in an article where the author studied the structure of solvation shell . So do you think it is possible to do that GROMACS? Regards, Sujith. On Thu, May 22, 2014 at 9:31 PM, Chandan Choudhury iitd...@gmail.comwrote: Hi Sujith, g_rdf is the tool you need. Chandan On Thu, May 22, 2014 at 8:18 PM, sujithkakkat . sujithk...@gmail.com wrote: Hello, I would like to know if it is possible to plot the RDF of water molecules belonging to the solvation shell of a solute. I mean, I want to know the effect of the solute on the water arrangement in the solvation shell. Is there a way to do this? Regards, Sujith. -- 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. -- -- Chandan Kumar Choudhury National Chemical Laboratory, Pune India -- 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.
