[gmx-users] Re: gmx-users Digest, Vol 114, Issue 75
Not working is too vague a symptom for anyone to guess what the problem is, sorry. Mark On Oct 24, 2013 9:39 AM, Santu Biswas santu.biswa...@gmail.com wrote: dear users, I am performing 500ps mdrun in vacuum for polypeptide(formed by 10-residues leucine) using gromacs_4.5.5(double- precision) using opls-aa/L force field.Input file for 500ps mdrun is given below title= peptide in vaccum cpp= /lib/cpp ; RUN CONTROL integrator = md comm_mode= ANGULAR nsteps = 50 dt= 0.001 ; NEIGHBOR SEARCHING nstlist = 0 ns_type = simple pbc = no rlist = 0 ; OUTPUT CONTROL nstxout = 1000 nstvout = 1000 nstxtcout = 0 nstlog= 1000 constraints = none nstenergy = 1000 ; OPTION FOR ELECTROSTATIC AND VDW rcoulomb = 0 ; Method for doing Van der Waals rvdw= 0 ; OPTIONS FOR WEAK COUPLING ALGORITHMS tcoupl = V-rescale tc_grps= Protein tau_t= 0.1 ref_t = 300 gen_vel= yes gen_temp = 300 Using the 500ps trajectory if i run g_hbond_d for calculating the number of hydrogen bonds as a function of time using index file(where atom O and atom N H is used) it is not working. Also if i used g_rdf_d with pbc=no using the 500ps trajectory it is also not working. I do not know why this is happening. -- santu -- Thanks Mark for your reply. Using the 500ps trajectory i want to calculate the number of hydrogen bonds as a function of time in vacuum .For this calculation i have uesd g_hbond_d -f traj_0-500ps.trr -s 500ps.tpr -n index.ndx -num hbond-num.xvg -dist dist.xvg -ang angle.xvg With what groups? Can there be any hydrogen bonds between those groups? Is there a bug fixed in a version of g_hbond that isn't 2 years old? Did a shorter trajectory work because it took less time? Does doing only one of three analyses help things to work? You'd be much closer to a solution if you'd tried some simplifications and done some detective work already ;-) Programm was running .After 1 hour it was still running but there was no output. If I calculate the number of hydrogen bonds as a function of time in water (no vacuum) using the same command line then there was no problem. Same problem when I used g_rdf in vacuum.The commad line I have used g_rdf_4.5.5 -f traj.trr -s 500ps.tpr -n index.ndx -o rdf.xvg and also checked with -nopbc with the same command line. RDF of what, in vacuum? What groups did you use? The programm is running but in the output file nothing is written. If I used g_rdf in water using the same command line there was no problem. OK - but does your analysis make sense in vacuum? Mark Thanks Mark for your reply In the index file I mentioned C=O oxygen atom and N-H hydrogen atom. Now I want to calculate the distance between O atom and N-H hydrogen atom using g_rdf in vacuum. Similarly using the same index file I want to calculate the number of hydrogen bonds as a function of time in vacuum using g_hbond. Yes there is a H bond between C=O oxygen atom of i-th residue and N-H hydrogen of i+4-th residue. I also checked with shorter trajectory there is also same problem . Please let me know If there are any mistakes. - santu -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Charges in vacuum simulation
Hi all, I'm trying to run a vacuum simulation of my protein which has a non-zero charge. How to deal with this charge? Can I add counter ions in to my system? Would it be energetically stable? How can one bring a protein to its isoelectric point? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_hbond and g_rdf in vacuum
On 10/28/13 3:30 AM, Santu Biswas wrote: Not working is too vague a symptom for anyone to guess what the problem is, sorry. Mark On Oct 24, 2013 9:39 AM, Santu Biswas santu.biswa...@gmail.com wrote: dear users, I am performing 500ps mdrun in vacuum for polypeptide(formed by 10-residues leucine) using gromacs_4.5.5(double- precision) using opls-aa/L force field.Input file for 500ps mdrun is given below title= peptide in vaccum cpp= /lib/cpp ; RUN CONTROL integrator = md comm_mode= ANGULAR nsteps = 50 dt= 0.001 ; NEIGHBOR SEARCHING nstlist = 0 ns_type = simple pbc = no rlist = 0 ; OUTPUT CONTROL nstxout = 1000 nstvout = 1000 nstxtcout = 0 nstlog= 1000 constraints = none nstenergy = 1000 ; OPTION FOR ELECTROSTATIC AND VDW rcoulomb = 0 ; Method for doing Van der Waals rvdw= 0 ; OPTIONS FOR WEAK COUPLING ALGORITHMS tcoupl = V-rescale tc_grps= Protein tau_t= 0.1 ref_t = 300 gen_vel= yes gen_temp = 300 Using the 500ps trajectory if i run g_hbond_d for calculating the number of hydrogen bonds as a function of time using index file(where atom O and atom N H is used) it is not working. Also if i used g_rdf_d with pbc=no using the 500ps trajectory it is also not working. I do not know why this is happening. -- santu -- Thanks Mark for your reply. Using the 500ps trajectory i want to calculate the number of hydrogen bonds as a function of time in vacuum .For this calculation i have uesd g_hbond_d -f traj_0-500ps.trr -s 500ps.tpr -n index.ndx -num hbond-num.xvg -dist dist.xvg -ang angle.xvg With what groups? Can there be any hydrogen bonds between those groups? Is there a bug fixed in a version of g_hbond that isn't 2 years old? Did a shorter trajectory work because it took less time? Does doing only one of three analyses help things to work? You'd be much closer to a solution if you'd tried some simplifications and done some detective work already ;-) Programm was running .After 1 hour it was still running but there was no output. If I calculate the number of hydrogen bonds as a function of time in water (no vacuum) using the same command line then there was no problem. Same problem when I used g_rdf in vacuum.The commad line I have used g_rdf_4.5.5 -f traj.trr -s 500ps.tpr -n index.ndx -o rdf.xvg and also checked with -nopbc with the same command line. RDF of what, in vacuum? What groups did you use? The programm is running but in the output file nothing is written. If I used g_rdf in water using the same command line there was no problem. OK - but does your analysis make sense in vacuum? Mark Thanks Mark for your reply In the index file I mentioned C=O oxygen atom and N-H hydrogen atom. Now I want to calculate the distance between O atom and N-H hydrogen atom using g_rdf in vacuum. Similarly using the same index file I want to calculate the number of hydrogen bonds as a function of time in vacuum using g_hbond. Yes there is a H bond between C=O oxygen atom of i-th residue and N-H hydrogen of i+4-th residue. I also checked with shorter trajectory there is also same problem . Please let me know If there are any mistakes. Does your system have a non-zero size? That is, are all the box vectors a somewhat reasonable value? They are, of course, irrelevant for the simulation (assuming pbc = no for in vacuo), but for analysis, you need a sensible box. If you don't, you can recenter the trajectory using trjconv -box -center. -Justin -- == Justin A. Lemkul, Ph.D. 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 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] pdb2gmx conversion
Dear Users, Whenever i convert a protein.pdb file using the following command (pdb2gmx -f protein.pdb -o protein.gro/pdb -water spc) and thereafter visualise the output with either vmd or pymol, i get the first amino acid residue breaking from the main chain. Would anyone help me understand why this is happening? Thanks. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] pdb2gmx conversion
Hi Musyoka, I would guess that that is related to the input coordinates. A bit of EM should fix it. Cheers, Tsjerk On Mon, Oct 28, 2013 at 11:20 AM, MUSYOKA THOMMAS mutemibiochemis...@gmail.com wrote: Dear Users, Whenever i convert a protein.pdb file using the following command (pdb2gmx -f protein.pdb -o protein.gro/pdb -water spc) and thereafter visualise the output with either vmd or pymol, i get the first amino acid residue breaking from the main chain. Would anyone help me understand why this is happening? Thanks. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Charges in vacuum simulation
If in vacuum, I would add hydrogens via covalent bonds. Dr. Vitaly V. Chaban On Mon, Oct 28, 2013 at 10:29 AM, Richa Singh richa.s.rathor...@gmail.com wrote: Hi all, I'm trying to run a vacuum simulation of my protein which has a non-zero charge. How to deal with this charge? Can I add counter ions in to my system? Would it be energetically stable? How can one bring a protein to its isoelectric point? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Gromacs tutorials for binding free energy analysis
Hello dears I would liked to know which of the tutorials presented by Gromacs for binding free energy analysis (http://www.gromacs.org/Documentation/Tutorials) are based on LIE method? regards, Sajad -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Gromacs tutorials for binding free energy analysis
On 10/28/13 8:02 AM, Sajad Ahrari wrote: Hello dears I would liked to know which of the tutorials presented by Gromacs for binding free energy analysis (http://www.gromacs.org/Documentation/Tutorials) are based on LIE method? I would suggest you read them and see. I suspect none of them are, though. -Justin -- == Justin A. Lemkul, Ph.D. 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 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] PLUMED2 official release
Dear GROMACS users and developers, We are very pleased to announce that PLUMED2 is available at www.plumed-code.org. Version 2.0 is a complete rewrite, so there is no way to write a complete set of differences with respect to PLUMED. Here is a summary of the major differences: - The input is simpler and more error proof. Many checks are now performed in such a way that common errors are avoided. - The units are now the same for all MD codes. If you want to use different units than the default ones, you can now set them in the input file. - The analysis tools are now much more flexible. As an example of this it is now possible to write different collective variables with different frequencies - Many complex collective variables are considerably faster with respect to PLUMED1. In particular, all variables based on RMSD distances. - Centers of mass can be used as if they were atoms. Hence, unlike PLUMED1, you can use center of mass positions in ALL collective variables. - The virial contribution is now computed and passed to the MD code. Plumed can thus now be used to perform biased NPT simulations In addition, it is now much easier to contribute new functionality to the code because: - There is a much simpler interface between PLUMED and the MD codes. This makes it much easier to add PLUMED to a new MD code. - PLUMED2 is written in a C++ object oriented programming and it is fully compatible with the C++ standard library - PLUMED2 is based on a modular structure - An extensive developer and user documentations are provided with the code While PLUMED2 includes many more functionalities with respect to PLUMED1, some other are missing and will be implemented shortly. Check the User manual in the How tos section about how moving from PLUMED1 to PLUMED2. More information can be found in the PLUMED2 paper, available on arxiv: http://arxiv.org/abs/1310.0980 and on the Computer Physics Communications website: http://www.sciencedirect.com/science/article/pii/S0010465513003196 The PLUMED developers team.-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Suggestion for a project
Dear Gromacs Users I would like to suggest a project in free energy calculations which can be in cooperation. The project is to demonstrate a novel and interesting method to calculate free energy differences between two solvation/binding processes. The first simulations are rather simple (solvation) and it can be extended to (binding) and to demonstrating more theoretical parts. The requirements are experience in MD simulations and alchemical transformations and immediate availability. An experience in writing an article is an advantage. To my opinion the demonstrations is likely to lead to an article or to be combined with existing material into an article. Information on the method can be found at: http://arxiv.org/abs/1310.2112 People that are interested can contact me in the follwoing emails: asaf.fa...@weizmann.ac.il asaf.fa...@gmail.com Thanks, Best regards, Asaf-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] parmbsc0 force field
Hi GMX users I want to use parmbsc0 force field for G-quadruplex structures MD simulation, but I'm not sure, the amber99sb_parmbsc0.ff.tgz in the gromacs site(http://www.gromacs.org/Special:Search?search=parmbsc0ns=mainpath=) is the parmbsc0 force field. Please help me Sincerely Kiana -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] mdrun cpt
I have need to collect 100ns but I can collect only ~1ns (1000steps) per run. Since I dont have .trr files, I rely on .cpt files for restarts. For example, grompp -f md.mdp -c md_14.gro -t md_14.cpt -p system.top -o md_15 This runs into a problem when the run gets killed due to walltime limits. I now have a .xtc file which has run (say) 700 steps and a .cpt file which was last written at 600th step. - To set up the next run I use the .cpt file from 600th step. - Now during analysis if I want to center the protein and such, /trjconv/ needs an .xtc and .tpr file but not a .cpt file. So how does /trjconv/ know to stop at 600th step? If this has to be put in manually, it becomes cumbersome. Thoughts? On Sun, Oct 27, 2013 at 11:38 AM, Justin Lemkul jalem...@vt.edu wrote: On 10/27/13 9:37 AM, Pavan Ghatty wrote: Hello All, Is there a way to make mdrun put out .cpt file with the same frequency as a .xtc or .trr file. From here http://www.gromacs.org/**Documentation/How-tos/Doing_**Restartshttp://www.gromacs.org/Documentation/How-tos/Doing_RestartsI see that we can choose how often (time in mins) the .cpt file is written. But clearly if the frequency of output of .cpt (frequency in mins) and .xtc (frequency in simulation steps) do not match, it can create problems during analysis; especially in the event of frequent crashes. Also, I am not storing .trr file since I dont need that precision. I am using Gromacs 4.6.1. What problems are you experiencing? There is no need for .cpt frequency to be the same as .xtc frequency, because any duplicate frames should be handled elegantly when appending. -Justin -- ==** Justin A. Lemkul, Ph.D. 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 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] mdrun cpt
On Mon, Oct 28, 2013 at 4:27 PM, Pavan Ghatty pavan.grom...@gmail.comwrote: I have need to collect 100ns but I can collect only ~1ns (1000steps) per run. Since I dont have .trr files, I rely on .cpt files for restarts. For example, grompp -f md.mdp -c md_14.gro -t md_14.cpt -p system.top -o md_15 This runs into a problem when the run gets killed due to walltime limits. I now have a .xtc file which has run (say) 700 steps and a .cpt file which was last written at 600th step. You seem to have no need to use grompp, because you don't need to use a workflow that generates multiple .tpr files. Do the equivalent of what the restart page advises: mdrun -s topol.tpr -cpi state.cpt. Thus, make a .tpr for the whole 100ns run, and then keep doing mdrun -s whole-run -cpi whateverwaslast -deffnm whateversuitsyouthistime with or without -append, perhaps with -maxh, keeping whatever manual backups you feel necessary. Then perhaps concatenate your final trajectory files, according to your earlier choices. - To set up the next run I use the .cpt file from 600th step. - Now during analysis if I want to center the protein and such, /trjconv/ needs an .xtc and .tpr file but not a .cpt file. So how does /trjconv/ know to stop at 600th step? trjconv just operates on the contents of the trajectory file, as modified by things like -b -e and -dt. The .tpr just gives it context, such as atom names. You could give it a .tpr from any point during the run. Mark If this has to be put in manually, it becomes cumbersome. Thoughts? On Sun, Oct 27, 2013 at 11:38 AM, Justin Lemkul jalem...@vt.edu wrote: On 10/27/13 9:37 AM, Pavan Ghatty wrote: Hello All, Is there a way to make mdrun put out .cpt file with the same frequency as a .xtc or .trr file. From here http://www.gromacs.org/**Documentation/How-tos/Doing_**Restarts http://www.gromacs.org/Documentation/How-tos/Doing_RestartsI see that we can choose how often (time in mins) the .cpt file is written. But clearly if the frequency of output of .cpt (frequency in mins) and .xtc (frequency in simulation steps) do not match, it can create problems during analysis; especially in the event of frequent crashes. Also, I am not storing .trr file since I dont need that precision. I am using Gromacs 4.6.1. What problems are you experiencing? There is no need for .cpt frequency to be the same as .xtc frequency, because any duplicate frames should be handled elegantly when appending. -Justin -- ==** Justin A. Lemkul, Ph.D. 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 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Search http://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] parmbsc0 force field
On 10/28/13 10:06 AM, kiana moghaddam wrote: Hi GMX users I want to use parmbsc0 force field for G-quadruplex structures MD simulation, but I'm not sure, the amber99sb_parmbsc0.ff.tgz in the gromacs site(http://www.gromacs.org/Special:Search?search=parmbsc0ns=mainpath=) is the parmbsc0 force field. Based on the name, it probably is. Check its contents against the relevant literature to be sure (minding unit conversion, of course). -Justin -- == Justin A. Lemkul, Ph.D. 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 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] How can I increase maximum number of pulling step for energy minimization?
Hi gromacs users: I use gromacs 4.5.6 for energy minimization with steepest descent method for ubiquitin pulling simulation with pulling step for applying displacement. For that simulation, I should repeat pulling and minimization process. I need 10^4 pulling step calculation to get fully unfolded structure, but the calculation stops at 503 pulling step with follow error message. = Source code file: futil.c, line: 489 File input/output error: abc.edr For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Sorry! You were supposed to get help about: mpi-abort But I couldn't open the help file: /usr/local/share/openmpi/help-mpi-api.txt: Too many open files. Sorry! -- = I open the futil.c line: 489, and that line is as follows. = gmx_file(buf); = However, I cannot catch what should I change to that line. If you have any ideas, please let me know. Sincerely, Chan -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] mdrun cpt
Mark, The problem with one .tpr file set for 100ns is that when job number (say) 4 hits the wall limit, it crashes and never gets a chance to submit the next job. So it's not really automated. Now I could initiate job 5 before /mdrun/ in job 4's script and hold job 5 till job 4 ends. But the PBS queuing system is sometime weird and takes a bit of time to recognize a job and give back its jobID. So I could submit job 5 but be unable to change its status to /hold/ because PBS does not return its ID. Another problem is that if resources are available, job 5 could start before I ever get a chance to /hold/ it. On Mon, Oct 28, 2013 at 11:47 AM, Mark Abraham mark.j.abra...@gmail.comwrote: On Mon, Oct 28, 2013 at 4:27 PM, Pavan Ghatty pavan.grom...@gmail.com wrote: I have need to collect 100ns but I can collect only ~1ns (1000steps) per run. Since I dont have .trr files, I rely on .cpt files for restarts. For example, grompp -f md.mdp -c md_14.gro -t md_14.cpt -p system.top -o md_15 This runs into a problem when the run gets killed due to walltime limits. I now have a .xtc file which has run (say) 700 steps and a .cpt file which was last written at 600th step. You seem to have no need to use grompp, because you don't need to use a workflow that generates multiple .tpr files. Do the equivalent of what the restart page advises: mdrun -s topol.tpr -cpi state.cpt. Thus, make a .tpr for the whole 100ns run, and then keep doing mdrun -s whole-run -cpi whateverwaslast -deffnm whateversuitsyouthistime with or without -append, perhaps with -maxh, keeping whatever manual backups you feel necessary. Then perhaps concatenate your final trajectory files, according to your earlier choices. - To set up the next run I use the .cpt file from 600th step. - Now during analysis if I want to center the protein and such, /trjconv/ needs an .xtc and .tpr file but not a .cpt file. So how does /trjconv/ know to stop at 600th step? trjconv just operates on the contents of the trajectory file, as modified by things like -b -e and -dt. The .tpr just gives it context, such as atom names. You could give it a .tpr from any point during the run. Mark If this has to be put in manually, it becomes cumbersome. Thoughts? On Sun, Oct 27, 2013 at 11:38 AM, Justin Lemkul jalem...@vt.edu wrote: On 10/27/13 9:37 AM, Pavan Ghatty wrote: Hello All, Is there a way to make mdrun put out .cpt file with the same frequency as a .xtc or .trr file. From here http://www.gromacs.org/**Documentation/How-tos/Doing_**Restarts http://www.gromacs.org/Documentation/How-tos/Doing_RestartsI see that we can choose how often (time in mins) the .cpt file is written. But clearly if the frequency of output of .cpt (frequency in mins) and .xtc (frequency in simulation steps) do not match, it can create problems during analysis; especially in the event of frequent crashes. Also, I am not storing .trr file since I dont need that precision. I am using Gromacs 4.6.1. What problems are you experiencing? There is no need for .cpt frequency to be the same as .xtc frequency, because any duplicate frames should be handled elegantly when appending. -Justin -- ==** Justin A. Lemkul, Ph.D. 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 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Search http://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the
[gmx-users] Obtaining trajectory coordinates at all dt
Hello, I have couple objectives as part of an analysis of my simulated system. And I would like some opinions on the tools to use to achieve it. I have the following interest in my system: 1) Find the probability distribution (density) of bond angle on my molecule between (i.e atom 12, 2,3 , 13, etc) as a function of time step, essentially, the equilibrium angle. [would I use g_chi for such analysis? ] 2) I want the above result in an excel spreadsheet, is there a way to obtain it as a spreadsheet? Or I can only get a plot representation as a function of time? Please share your expertise and opinions. Thank you. Xu Huang -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] mdrun cpt
No this isn't a problem. You can use job names under the -hold_jid flag. As long as you change the job name in the submit script between submissions this isn't a problem. You could have a submit script for job 4 with -N md_job4 and -hold_jid md_job3 then change these to -N md_job5 and -hold_jid md_job4 for the next job. Then you can submit job 5 as soon as you have made this change which will be within seconds of submitting job 4. Mark, The problem with one .tpr file set for 100ns is that when job number (say) 4 hits the wall limit, it crashes and never gets a chance to submit the next job. So it's not really automated. Now I could initiate job 5 before /mdrun/ in job 4's script and hold job 5 till job 4 ends. But the PBS queuing system is sometime weird and takes a bit of time to recognize a job and give back its jobID. So I could submit job 5 but be unable to change its status to /hold/ because PBS does not return its ID. Another problem is that if resources are available, job 5 could start before I ever get a chance to /hold/ it. On Mon, Oct 28, 2013 at 11:47 AM, Mark Abraham mark.j.abra...@gmail.comwrote: On Mon, Oct 28, 2013 at 4:27 PM, Pavan Ghatty pavan.grom...@gmail.com wrote: I have need to collect 100ns but I can collect only ~1ns (1000steps) per run. Since I dont have .trr files, I rely on .cpt files for restarts. For example, grompp -f md.mdp -c md_14.gro -t md_14.cpt -p system.top -o md_15 This runs into a problem when the run gets killed due to walltime limits. I now have a .xtc file which has run (say) 700 steps and a .cpt file which was last written at 600th step. You seem to have no need to use grompp, because you don't need to use a workflow that generates multiple .tpr files. Do the equivalent of what the restart page advises: mdrun -s topol.tpr -cpi state.cpt. Thus, make a .tpr for the whole 100ns run, and then keep doing mdrun -s whole-run -cpi whateverwaslast -deffnm whateversuitsyouthistime with or without -append, perhaps with -maxh, keeping whatever manual backups you feel necessary. Then perhaps concatenate your final trajectory files, according to your earlier choices. - To set up the next run I use the .cpt file from 600th step. - Now during analysis if I want to center the protein and such, /trjconv/ needs an .xtc and .tpr file but not a .cpt file. So how does /trjconv/ know to stop at 600th step? trjconv just operates on the contents of the trajectory file, as modified by things like -b -e and -dt. The .tpr just gives it context, such as atom names. You could give it a .tpr from any point during the run. Mark If this has to be put in manually, it becomes cumbersome. Thoughts? On Sun, Oct 27, 2013 at 11:38 AM, Justin Lemkul jalem...@vt.edu wrote: On 10/27/13 9:37 AM, Pavan Ghatty wrote: Hello All, Is there a way to make mdrun put out .cpt file with the same frequency as a .xtc or .trr file. From here http://www.gromacs.org/**Documentation/How-tos/Doing_**Restarts http://www.gromacs.org/Documentation/How-tos/Doing_RestartsI see that we can choose how often (time in mins) the .cpt file is written. But clearly if the frequency of output of .cpt (frequency in mins) and .xtc (frequency in simulation steps) do not match, it can create problems during analysis; especially in the event of frequent crashes. Also, I am not storing .trr file since I dont need that precision. I am using Gromacs 4.6.1. What problems are you experiencing? There is no need for .cpt frequency to be the same as .xtc frequency, because any duplicate frames should be handled elegantly when appending. -Justin -- ==** Justin A. Lemkul, Ph.D. 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 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Search http://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before
Re: [gmx-users] mdrun cpt
Aah yes of course. Thanks James. On Mon, Oct 28, 2013 at 3:16 PM, jkrie...@mrc-lmb.cam.ac.uk wrote: No this isn't a problem. You can use job names under the -hold_jid flag. As long as you change the job name in the submit script between submissions this isn't a problem. You could have a submit script for job 4 with -N md_job4 and -hold_jid md_job3 then change these to -N md_job5 and -hold_jid md_job4 for the next job. Then you can submit job 5 as soon as you have made this change which will be within seconds of submitting job 4. Mark, The problem with one .tpr file set for 100ns is that when job number (say) 4 hits the wall limit, it crashes and never gets a chance to submit the next job. So it's not really automated. Now I could initiate job 5 before /mdrun/ in job 4's script and hold job 5 till job 4 ends. But the PBS queuing system is sometime weird and takes a bit of time to recognize a job and give back its jobID. So I could submit job 5 but be unable to change its status to /hold/ because PBS does not return its ID. Another problem is that if resources are available, job 5 could start before I ever get a chance to /hold/ it. On Mon, Oct 28, 2013 at 11:47 AM, Mark Abraham mark.j.abra...@gmail.comwrote: On Mon, Oct 28, 2013 at 4:27 PM, Pavan Ghatty pavan.grom...@gmail.com wrote: I have need to collect 100ns but I can collect only ~1ns (1000steps) per run. Since I dont have .trr files, I rely on .cpt files for restarts. For example, grompp -f md.mdp -c md_14.gro -t md_14.cpt -p system.top -o md_15 This runs into a problem when the run gets killed due to walltime limits. I now have a .xtc file which has run (say) 700 steps and a .cpt file which was last written at 600th step. You seem to have no need to use grompp, because you don't need to use a workflow that generates multiple .tpr files. Do the equivalent of what the restart page advises: mdrun -s topol.tpr -cpi state.cpt. Thus, make a .tpr for the whole 100ns run, and then keep doing mdrun -s whole-run -cpi whateverwaslast -deffnm whateversuitsyouthistime with or without -append, perhaps with -maxh, keeping whatever manual backups you feel necessary. Then perhaps concatenate your final trajectory files, according to your earlier choices. - To set up the next run I use the .cpt file from 600th step. - Now during analysis if I want to center the protein and such, /trjconv/ needs an .xtc and .tpr file but not a .cpt file. So how does /trjconv/ know to stop at 600th step? trjconv just operates on the contents of the trajectory file, as modified by things like -b -e and -dt. The .tpr just gives it context, such as atom names. You could give it a .tpr from any point during the run. Mark If this has to be put in manually, it becomes cumbersome. Thoughts? On Sun, Oct 27, 2013 at 11:38 AM, Justin Lemkul jalem...@vt.edu wrote: On 10/27/13 9:37 AM, Pavan Ghatty wrote: Hello All, Is there a way to make mdrun put out .cpt file with the same frequency as a .xtc or .trr file. From here http://www.gromacs.org/**Documentation/How-tos/Doing_**Restarts http://www.gromacs.org/Documentation/How-tos/Doing_RestartsI see that we can choose how often (time in mins) the .cpt file is written. But clearly if the frequency of output of .cpt (frequency in mins) and .xtc (frequency in simulation steps) do not match, it can create problems during analysis; especially in the event of frequent crashes. Also, I am not storing .trr file since I dont need that precision. I am using Gromacs 4.6.1. What problems are you experiencing? There is no need for .cpt frequency to be the same as .xtc frequency, because any duplicate frames should be handled elegantly when appending. -Justin -- ==** Justin A. Lemkul, Ph.D. 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 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Search http://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read
Re: [gmx-users] mdrun cpt
You're welcome On 28 Oct 2013, at 20:03, Pavan Ghatty pavan.grom...@gmail.com wrote: Aah yes of course. Thanks James. On Mon, Oct 28, 2013 at 3:16 PM, jkrie...@mrc-lmb.cam.ac.uk wrote: No this isn't a problem. You can use job names under the -hold_jid flag. As long as you change the job name in the submit script between submissions this isn't a problem. You could have a submit script for job 4 with -N md_job4 and -hold_jid md_job3 then change these to -N md_job5 and -hold_jid md_job4 for the next job. Then you can submit job 5 as soon as you have made this change which will be within seconds of submitting job 4. Mark, The problem with one .tpr file set for 100ns is that when job number (say) 4 hits the wall limit, it crashes and never gets a chance to submit the next job. So it's not really automated. Now I could initiate job 5 before /mdrun/ in job 4's script and hold job 5 till job 4 ends. But the PBS queuing system is sometime weird and takes a bit of time to recognize a job and give back its jobID. So I could submit job 5 but be unable to change its status to /hold/ because PBS does not return its ID. Another problem is that if resources are available, job 5 could start before I ever get a chance to /hold/ it. On Mon, Oct 28, 2013 at 11:47 AM, Mark Abraham mark.j.abra...@gmail.comwrote: On Mon, Oct 28, 2013 at 4:27 PM, Pavan Ghatty pavan.grom...@gmail.com wrote: I have need to collect 100ns but I can collect only ~1ns (1000steps) per run. Since I dont have .trr files, I rely on .cpt files for restarts. For example, grompp -f md.mdp -c md_14.gro -t md_14.cpt -p system.top -o md_15 This runs into a problem when the run gets killed due to walltime limits. I now have a .xtc file which has run (say) 700 steps and a .cpt file which was last written at 600th step. You seem to have no need to use grompp, because you don't need to use a workflow that generates multiple .tpr files. Do the equivalent of what the restart page advises: mdrun -s topol.tpr -cpi state.cpt. Thus, make a .tpr for the whole 100ns run, and then keep doing mdrun -s whole-run -cpi whateverwaslast -deffnm whateversuitsyouthistime with or without -append, perhaps with -maxh, keeping whatever manual backups you feel necessary. Then perhaps concatenate your final trajectory files, according to your earlier choices. - To set up the next run I use the .cpt file from 600th step. - Now during analysis if I want to center the protein and such, /trjconv/ needs an .xtc and .tpr file but not a .cpt file. So how does /trjconv/ know to stop at 600th step? trjconv just operates on the contents of the trajectory file, as modified by things like -b -e and -dt. The .tpr just gives it context, such as atom names. You could give it a .tpr from any point during the run. Mark If this has to be put in manually, it becomes cumbersome. Thoughts? On Sun, Oct 27, 2013 at 11:38 AM, Justin Lemkul jalem...@vt.edu wrote: On 10/27/13 9:37 AM, Pavan Ghatty wrote: Hello All, Is there a way to make mdrun put out .cpt file with the same frequency as a .xtc or .trr file. From here http://www.gromacs.org/**Documentation/How-tos/Doing_**Restarts http://www.gromacs.org/Documentation/How-tos/Doing_RestartsI see that we can choose how often (time in mins) the .cpt file is written. But clearly if the frequency of output of .cpt (frequency in mins) and .xtc (frequency in simulation steps) do not match, it can create problems during analysis; especially in the event of frequent crashes. Also, I am not storing .trr file since I dont need that precision. I am using Gromacs 4.6.1. What problems are you experiencing? There is no need for .cpt frequency to be the same as .xtc frequency, because any duplicate frames should be handled elegantly when appending. -Justin -- ==** Justin A. Lemkul, Ph.D. 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 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Search http://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org
[gmx-users] Failure in MD run without any error
DearGromacs users I have encountered something strange. I have installed Red Hat Enterprise Linux 6.1 6.2 on two machines recently and then lam 7.1.4, fftw 3.3.2 and Gromacs 4.5.5 . During linux installation, everything went well I didn`t face any complain or receiving any error, as well as in lam, fftw and Gromacs installation, But when I run an MD job on both of these machines, at first everything seems normal but after some steps ( usually multi thousands steps), the job doesn`t proceed. Log file does not show any change or there is no error. Obviously the job is stopped while terminal shows all the processors are 100% busy. I have also reinstalled the linux and the mentioned programs too but it did not solve the problem. I don`t have any idea what the problem is. Any comment or suggestion would be highly appreciated. Thanks in advance, Niloofar -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Replica Exchange with Solute Tempering
Greetings, I would also be interested in an example of using REST via Hamiltonian REMD in the current gromacs build. I'm particularly interested in enhanced conformational sampling of 160-270 residue proteins. As it stands, I've been unable to achieve any appreciable exchange probability in coulomb or vdw lambdas without resorting to changing the lambda values by +/- 0.02 or less and am hoping ST will allow me to increase the spacing between lambdas. Thanks for any help, Andrew On Sat, Oct 26, 2013 at 9:45 PM, HANNIBAL LECTER hanniballecte...@gmail.com wrote: Hi I had tried using gromacs-4.6.1 to perform solute tempering. If you go through terakawa's paper you have to describe the lambdas corresponding to the temperatures. In your topology file define the params corresponding to the two end states l=0 and l=1. Then define vdw, bonded and coulomb lambdas in the mdp file. The format is very well described in the manual. Then just the regular -replex syntax would perform solute tempering. However, the free energy module required to perform this, is extremely slow. On Oct 26, 2013 8:46 PM, David Osguthorpe david.osgutho...@gmail.com wrote: On Sat, Oct 26, 2013 at 06:06:59PM -0400, Michael Shirts wrote: Hi, all- Rest essentially scales the solute-solvent interactions, but maintains the solute-solute interactions. This can be done solely with Hamiltonian replica exchange, which is in 4.6. It's a bit tricky, though. We plan on having something that does this automatically in 5.0 or 5.1, but it's not there yet. What do you intend to do? It could be that there's a better way to do what you want to do with Hamiltonian replica exchange, as well. Sorry - yes Im looking for an example of how to do REST via Hamiltonian replica exchange Ive seen the papers by Moors (Improved Replica Exchange Method for Native-State Protein Sampling) and Terekawa (On easy implementation of a variant of the replica exchange with solute tempering in GROMACS) and followed some of the gromacs user list discussions from 2011 on REST simulations As you say, it looks like its a bit tricky so was hoping there was a toy example somewhere Thanks David -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- -Andrew Ritchie -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Failure in MD run without any error
Hi, Hard to know. LAM was discontinued over 4 years ago. You could have a flaky file system. Unless you're trying to run a jobsover both machines over network like Infiniband, you don't even want to use an external MPI library - single-node performance with built-in thread-MPI will give much better value. Mark On Mon, Oct 28, 2013 at 9:12 PM, niloofar niknam niloofae_nik...@yahoo.comwrote: DearGromacs users I have encountered something strange. I have installed Red Hat Enterprise Linux 6.1 6.2 on two machines recently and then lam 7.1.4, fftw 3.3.2 and Gromacs 4.5.5 . During linux installation, everything went well I didn`t face any complain or receiving any error, as well as in lam, fftw and Gromacs installation, But when I run an MD job on both of these machines, at first everything seems normal but after some steps ( usually multi thousands steps), the job doesn`t proceed. Log file does not show any change or there is no error. Obviously the job is stopped while terminal shows all the processors are 100% busy. I have also reinstalled the linux and the mentioned programs too but it did not solve the problem. I don`t have any idea what the problem is. Any comment or suggestion would be highly appreciated. Thanks in advance, Niloofar -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] mdrun cpt
On Mon, Oct 28, 2013 at 7:53 PM, Pavan Ghatty pavan.grom...@gmail.comwrote: Mark, The problem with one .tpr file set for 100ns is that when job number (say) 4 hits the wall limit, it crashes and never gets a chance to submit the next job. So it's not really automated. That's why I suggested -maxh, so you can have an orderly shutdown. (Though if a job can get suspended, that won't always help, because mdrun can't find out about the suspension...) Now I could initiate job 5 before /mdrun/ in job 4's script and hold job 5 till job 4 ends. Sure - read your PBS docs and find the environment variable to read so that job 4 knows its ID so it can submit job 5 with an afterok hold on job 4 on it. But don't tell your sysadmins where I live. ;-) Seriously, if you live on this edge, you could spam infinite jobs, which tends to get your account cut off. That's why you want the afterok hold - you only want the next job to start if the exit code from the first script correctly indicates that mdrun exited correctly. Test carefully! Mark But the PBS queuing system is sometime weird and takes a bit of time to recognize a job and give back its jobID. So I could submit job 5 but be unable to change its status to /hold/ because PBS does not return its ID. Another problem is that if resources are available, job 5 could start before I ever get a chance to /hold/ it. On Mon, Oct 28, 2013 at 11:47 AM, Mark Abraham mark.j.abra...@gmail.com wrote: On Mon, Oct 28, 2013 at 4:27 PM, Pavan Ghatty pavan.grom...@gmail.com wrote: I have need to collect 100ns but I can collect only ~1ns (1000steps) per run. Since I dont have .trr files, I rely on .cpt files for restarts. For example, grompp -f md.mdp -c md_14.gro -t md_14.cpt -p system.top -o md_15 This runs into a problem when the run gets killed due to walltime limits. I now have a .xtc file which has run (say) 700 steps and a .cpt file which was last written at 600th step. You seem to have no need to use grompp, because you don't need to use a workflow that generates multiple .tpr files. Do the equivalent of what the restart page advises: mdrun -s topol.tpr -cpi state.cpt. Thus, make a .tpr for the whole 100ns run, and then keep doing mdrun -s whole-run -cpi whateverwaslast -deffnm whateversuitsyouthistime with or without -append, perhaps with -maxh, keeping whatever manual backups you feel necessary. Then perhaps concatenate your final trajectory files, according to your earlier choices. - To set up the next run I use the .cpt file from 600th step. - Now during analysis if I want to center the protein and such, /trjconv/ needs an .xtc and .tpr file but not a .cpt file. So how does /trjconv/ know to stop at 600th step? trjconv just operates on the contents of the trajectory file, as modified by things like -b -e and -dt. The .tpr just gives it context, such as atom names. You could give it a .tpr from any point during the run. Mark If this has to be put in manually, it becomes cumbersome. Thoughts? On Sun, Oct 27, 2013 at 11:38 AM, Justin Lemkul jalem...@vt.edu wrote: On 10/27/13 9:37 AM, Pavan Ghatty wrote: Hello All, Is there a way to make mdrun put out .cpt file with the same frequency as a .xtc or .trr file. From here http://www.gromacs.org/**Documentation/How-tos/Doing_**Restarts http://www.gromacs.org/Documentation/How-tos/Doing_RestartsI see that we can choose how often (time in mins) the .cpt file is written. But clearly if the frequency of output of .cpt (frequency in mins) and .xtc (frequency in simulation steps) do not match, it can create problems during analysis; especially in the event of frequent crashes. Also, I am not storing .trr file since I dont need that precision. I am using Gromacs 4.6.1. What problems are you experiencing? There is no need for .cpt frequency to be the same as .xtc frequency, because any duplicate frames should be handled elegantly when appending. -Justin -- ==** Justin A. Lemkul, Ph.D. 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 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Search http://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't
Re: [gmx-users] Re: gmx-users Digest, Vol 114, Issue 15
On Mon, Oct 28, 2013 at 8:04 PM, Hari Pandey hariche...@yahoo.com wrote: Dear Gromacs Users, First, I would like to thank Dr. Lemkul for reply. My problem description is as follows: I am using CHARMM36 forcefield to equilibrate of AOT. when I add the mass of all atoms from topology, it gives me 444.5 which is correct but when I run the script Justin asked you about your atom names, but somehow you have forgotten to answer him :-) editconf -c -f A.gro -o A.gro -density 1000 -bt cubic -box 5 -d 0.1 . It display incorrect value for mass of input. The mass of input should be 444.5 . The out come of above script is: Volume: 125 nm^3, corresponds to roughly 56200 electrons No velocities found system size : 0.215 0.234 0.157 (nm) diameter: 0.287 (nm) center : 2.500 2.500 2.500 (nm) box vectors : 5.000 5.000 5.000 (nm) box angles : 90.00 90.00 90.00 (degrees) box volume : 125.00 (nm^3) WARNING: masses and atomic (Van der Waals) radii will be determined based on residue and atom names. These numbers can deviate from the correct mass and radius of the atom type. editconf only has a .gro file, so it does not know about any atom types, or bonds, so it is not worth trying to write code to guess correctly whether HG1 is the first hydrogen on the gamma carbon, or the first mercury, etc. We do write a warning message, but sometimes people don't read them. Mark Volume of input 125 (nm^3) Massof input 967.25 (a.m.u.) Density of input 12.8493 (g/l) Scaling all box vectors by 0.234221 new system size : 0.050 0.055 0.037 shift : 1.914 1.914 1.914 (nm) new center : 2.500 2.500 2.500 (nm) new box vectors : 5.000 5.000 5.000 (nm) new box angles : 90.00 90.00 90.00 (degrees) new box volume : 125.00(nm^3) Here we can see that mass of input is 967.25 which is far beyond the reality. this will cause error in density and all other mass dependent parameters. Please help me how do I come over to this error Thank you so much for you kind help Hari -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] How can I increase maximum number of pulling step for energy minimization?
On 10/28/13 1:59 PM, Gwonchan Yoon wrote: Hi gromacs users: I use gromacs 4.5.6 for energy minimization with steepest descent method for ubiquitin pulling simulation with pulling step for applying displacement. For that simulation, I should repeat pulling and minimization process. I need 10^4 pulling step calculation to get fully unfolded structure, but the calculation stops at 503 pulling step with follow error message. = Source code file: futil.c, line: 489 File input/output error: abc.edr For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Sorry! You were supposed to get help about: mpi-abort But I couldn't open the help file: /usr/local/share/openmpi/help-mpi-api.txt: Too many open files. Sorry! -- = I open the futil.c line: 489, and that line is as follows. = gmx_file(buf); = However, I cannot catch what should I change to that line. If you have any ideas, please let me know. You shouldn't change the source to get around the error. There's nothing really that you can do there. I/O errors happen when files cannot be read or written to, either because of permission problems, full disk, file system glitches, simulation crashing, etc. -Justin -- == Justin A. Lemkul, Ph.D. 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 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: gmx-users Digest, Vol 114, Issue 15
Thank you so much Mark. I still did not understand. More detaily. Atomtypes are only following: atomtypes.atp:: H 1.00800 ; polar H DUM 0.0 ; dummy atom HAL1 1.008000 ; alphatic proton HAL2 1.008000 ; alphatic proton HAL3 1.008000 ; alphatic proton CTL1 12.011000 ; carbonyl C (acetic acid/methyl acetate);;; CTL1 12.011000 ; sp3 carbon with 1 H (-CH1-) CTL2 12.011000 ; carbon of methylene group (-CH2-) CTL3 12.011000 ; carbon of methyl group (-CH3) OBL 15.999400 ; acetic acid carboxyl oxygen (e. to protein OB) OCL 15.999400 ; acetate oxygen OSL 15.999400 ; ester oxygen O2L 15.999400 ; Nucleic acid =O in phosphate or sulfate SL 32.06 ; Sulfate sulfur NA 22.989770 ; FOR sodium ion MR.rtp: S SL 1.3600 0 OS1 O2L -0.6000 0 OS2 O2L -0.6000 0 OS3 O2L -0.6000 0 C1 CTL1 -0.1900 0 H1 HAL1 0.0900 0 C2 CTL2 -0.1800 1 H2 HAL2 0.0900 1 H3 HAL2 0.0900 1 C3 CL 0.6300 2 ; O1 OBL -0.5200 2 O2 OSL -0.3400 2 C4 CTL2 -0.1800 3 H4 HAL2 0.0900 3 H5 HAL2 0.0900 3 C5 CTL1 -0.0900 4 H6 HAL1 0.0900 4 C6 CTL2 -0.1800 5 H7 HAL2 0.0900 5 H8 HAL2 0.0900 5 C7 CTL2 -0.1800 6 H9 HAL2 0.0900 6 H10 HAL2 0.0900 6 C8 CTL2 -0.1800 7 H11 HAL2 0.0900 7 H12 HAL2 0.0900 7 C9 CTL3 -0.2700 8 H13 HAL3 0.0900 8 H14 HAL3 0.0900 8 H15 HAL3 0.0900 8 C10 CTL2 -0.1800 9 H16 HAL2 0.0900 9 H17 HAL2 0.0900 9 C11 CTL3 -0.2700 10 H18 HAL3 0.0900 10 H19 HAL3 0.0900 10 H20 HAL3 0.0900 10 C12 CL 0.6300 11 ; O3 OBL -0.5200 11 O4 OSL -0.3400 11 C13 CTL2 -0.1800 12 H21 HAL2 0.0900 12 H22 HAL2 0.0900 12 C14 CTL1 -0.0900 13 H23 HAL1 0.0900 13 C15 CTL2 -0.1800 14 H24 HAL2 0.0900 14 H25 HAL2 0.0900 14 C16 CTL2 -0.1800 15 H26 HAL2 0.0900 15 H27 HAL2 0.0900 15 C17 CTL2 -0.1800 16 I have A.pdb and I got A.gro using this force field. Some part of A.pdb:: REMARK Created: Fri Jun 08 12:50:20 Paris, Madrid (heure d'?t?) 2007 CRYST1 8.760 8.760 8.760 90.00 90.00 90.00 P1 1 MODEL 1 ATOM 1 S AOT 151 6.864 -6.902 0.078 1.00 0.00 ATOM 2 OS1 AOT 151 7.820 -5.791 -0.815 1.00 0.00 ATOM 3 OS2 AOT 151 5.369 -7.134 -0.714 1.00 0.00 ATOM 4 OS3 AOT 151 6.589 -6.277 1.657 1.00 0.00 ATOM 5 C1 AOT 151 7.728 -8.482 0.196 1.00 0.00 ATOM 6 H1 AOT 151 8.702 -8.326 0.676 1.00 0.00 ATOM 7 C2 AOT 151 7.952 -8.937 -1.268 1.00 0.00 ATOM 8 H2 AOT 151 7.067 -9.120 -1.697 1.00 0.00 ATOM 9 H3 AOT 151 8.423 -8.212 -1.771 1.00 0.00 ATOM 10 C3 AOT 151 6.874 -9.526 1.026 1.00 0.00 ATOM 11 O1 AOT 151 6.661 -9.024 2.356 1.00 0.00 ATOM 12 O2 AOT 151 7.505 -10.821 1.169 1.00 0.00 ATOM 13 C4 AOT 151 6.679
Re: [gmx-users] Re: gmx-users Digest, Vol 114, Issue 15
On 10/28/13 7:41 PM, Hari Pandey wrote: Thank you so much Mark. I still did not understand. More detaily. Atomtypes are only following: atomtypes.atp:: H 1.00800 ; polar H DUM0.0 ; dummy atom HAL1 1.008000 ; alphatic proton HAL2 1.008000 ; alphatic proton HAL3 1.008000 ; alphatic proton CTL1 12.011000 ; carbonyl C (acetic acid/methyl acetate);;; CTL1 12.011000 ; sp3 carbon with 1 H (-CH1-) CTL2 12.011000 ; carbon of methylene group (-CH2-) CTL3 12.011000 ; carbon of methyl group (-CH3) OBL15.999400 ; acetic acid carboxyl oxygen (e. to protein OB) OCL15.999400 ; acetate oxygen OSL15.999400 ; ester oxygen O2L 15.999400 ; Nucleic acid =O in phosphate or sulfate SL 32.06 ; Sulfate sulfur NA 22.989770; FOR sodium ion MR.rtp: SSL 1.3600 0 OS1 O2L -0.6000 0 OS2 O2L -0.6000 0 OS3 O2L -0.6000 0 C1 CTL1-0.1900 0 H1 HAL10.0900 0 C2 CTL2-0.1800 1 H2 HAL20.0900 1 H3 HAL20.0900 1 C3 CL 0.6300 2 ; O1 OBL -0.5200 2 O2 OSL -0.3400 2 C4 CTL2-0.1800 3 H4 HAL20.0900 3 H5 HAL20.0900 3 C5 CTL1-0.0900 4 H6 HAL10.0900 4 C6 CTL2-0.1800 5 H7 HAL20.0900 5 H8 HAL20.0900 5 C7 CTL2-0.1800 6 H9 HAL20.0900 6 H10 HAL20.0900 6 C8 CTL2-0.1800 7 H11 HAL20.0900 7 H12 HAL20.0900 7 C9 CTL3-0.2700 8 H13 HAL30.0900 8 H14 HAL30.0900 8 H15 HAL30.0900 8 C10 CTL2-0.1800 9 H16 HAL20.0900 9 H17 HAL20.0900 9 C11 CTL3-0.2700 10 H18 HAL30.0900 10 H19 HAL30.0900 10 H20 HAL30.0900 10 C12 CL 0.6300 11 ; O3 OBL -0.5200 11 O4 OSL -0.3400 11 C13 CTL2-0.1800 12 H21 HAL20.0900 12 H22 HAL20.0900 12 C14 CTL1-0.0900 13 H23 HAL10.0900 13 C15 CTL2-0.1800 14 H24 HAL20.0900 14 H25 HAL20.0900 14 C16 CTL2-0.1800 15 H26 HAL20.0900 15 H27 HAL20.0900 15 C17 CTL2-0.1800 16 I have A.pdb and I got A.gro using this force field. Some part of A.pdb:: REMARK Created: Fri Jun 08 12:50:20 Paris, Madrid (heure d'?t?) 2007 CRYST1 8.760 8.760 8.760 90.00 90.00 90.00 P11 MODEL1 ATOM 1 S AOT 151 6.864 -6.902 0.078 1.00 0.00 ATOM 2 OS1 AOT 151 7.820 -5.791 -0.815 1.00 0.00 ATOM 3 OS2 AOT 151 5.369 -7.134 -0.714 1.00 0.00 ATOM 4 OS3 AOT 151 6.589 -6.277 1.657 1.00 0.00 ATOM 5 C1 AOT 151 7.728 -8.482 0.196 1.00 0.00 ATOM 6 H1 AOT 151 8.702 -8.326 0.676 1.00 0.00 ATOM 7 C2 AOT 151 7.952 -8.937 -1.268 1.00 0.00 ATOM 8 H2 AOT 151 7.067 -9.120 -1.697 1.00 0.00 ATOM 9 H3 AOT 151 8.423 -8.212 -1.771 1.00 0.00 ATOM 10 C3 AOT 151 6.874 -9.526 1.026 1.00 0.00 ATOM 11 O1 AOT 151 6.661 -9.024 2.356 1.00 0.00 ATOM 12 O2 AOT 151 7.505 -10.821 1.169 1.00 0.00 ATOM 13 C4 AOT 151 6.679 -11.663 1.968 1.00 0.00 ATOM 14 H4 AOT 151 5.837 -11.877 1.473 1.00 0.00 ATOM 15 H5 AOT 151 6.454 -11.200 2.825 1.00 0.00 ATOM 16 C5 AOT 151 7.443 -12.948 2.264 1.00 0.00 ATOM 17 H6 AOT 151 8.370 -12.683 2.786 1.00 0.00 ATOM 18 C6 AOT 151 6.520 -13.788 3.227 1.00 0.00 ATOM 19 H7 AOT 151 5.703 -14.049 2.713 1.00 0.00 ATOM 20 H8 AOT 151 6.258 -13.205 3.996 1.00 0.00 ATOM 21 C7 AOT 151 7.156 -15.071 3.796 1.00 0.00 ATOM 22 H9 AOT 151 7.386 -15.690 3.045 1.00 0.00 ATOM 23 H10 AOT 151 7.987 -14.835 4.300 1.00 0.00 ATOM
Re: [gmx-users] Re: gmx-users Digest, Vol 114, Issue 15
Many thanks to Dr.Lemkul Yes mass is 444 in my .top file and I did -density 1000 because then it will show the density also. I am wandering how do I find that which atom name mismatched. The forcefield folder is in my working directory and there are all files. atomtypes.atp is there and which contains the atom names which I posted last email Thanks for your regard Hari On Monday, October 28, 2013 4:50 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/28/13 7:41 PM, Hari Pandey wrote: Thank you so much Mark. I still did not understand. More detaily. Atomtypes are only following: atomtypes.atp:: H 1.00800 ; polar H DUM 0.0 ; dummy atom HAL1 1.008000 ; alphatic proton HAL2 1.008000 ; alphatic proton HAL3 1.008000 ; alphatic proton CTL1 12.011000 ; carbonyl C (acetic acid/methyl acetate);;; CTL1 12.011000 ; sp3 carbon with 1 H (-CH1-) CTL2 12.011000 ; carbon of methylene group (-CH2-) CTL3 12.011000 ; carbon of methyl group (-CH3) OBL 15.999400 ; acetic acid carboxyl oxygen (e. to protein OB) OCL 15.999400 ; acetate oxygen OSL 15.999400 ; ester oxygen O2L 15.999400 ; Nucleic acid =O in phosphate or sulfate SL 32.06 ; Sulfate sulfur NA 22.989770 ; FOR sodium ion MR.rtp: S SL 1.3600 0 OS1 O2L -0.6000 0 OS2 O2L -0.6000 0 OS3 O2L -0.6000 0 C1 CTL1 -0.1900 0 H1 HAL1 0.0900 0 C2 CTL2 -0.1800 1 H2 HAL2 0.0900 1 H3 HAL2 0.0900 1 C3 CL 0.6300 2 ; O1 OBL -0.5200 2 O2 OSL -0.3400 2 C4 CTL2 -0.1800 3 H4 HAL2 0.0900 3 H5 HAL2 0.0900 3 C5 CTL1 -0.0900 4 H6 HAL1 0.0900 4 C6 CTL2 -0.1800 5 H7 HAL2 0.0900 5 H8 HAL2 0.0900 5 C7 CTL2 -0.1800 6 H9 HAL2 0.0900 6 H10 HAL2 0.0900 6 C8 CTL2 -0.1800 7 H11 HAL2 0.0900 7 H12 HAL2 0.0900 7 C9 CTL3 -0.2700 8 H13 HAL3 0.0900 8 H14 HAL3 0.0900 8 H15 HAL3 0.0900 8 C10 CTL2 -0.1800 9 H16 HAL2 0.0900 9 H17 HAL2 0.0900 9 C11 CTL3 -0.2700 10 H18 HAL3 0.0900 10 H19 HAL3 0.0900 10 H20 HAL3 0.0900 10 C12 CL 0.6300 11 ; O3 OBL -0.5200 11 O4 OSL -0.3400 11 C13 CTL2 -0.1800 12 H21 HAL2 0.0900 12 H22 HAL2 0.0900 12 C14 CTL1 -0.0900 13 H23 HAL1 0.0900 13 C15 CTL2 -0.1800 14 H24 HAL2 0.0900 14 H25 HAL2 0.0900 14 C16 CTL2 -0.1800 15 H26 HAL2 0.0900 15 H27 HAL2 0.0900 15 C17 CTL2 -0.1800 16 I have A.pdb and I got A.gro using this force field. Some part of A.pdb:: REMARK Created: Fri Jun 08 12:50:20 Paris, Madrid (heure d'?t?) 2007 CRYST1 8.760 8.760 8.760 90.00 90.00 90.00 P1 1 MODEL 1 ATOM 1 S AOT 151 6.864 -6.902 0.078 1.00 0.00 ATOM 2 OS1 AOT 151 7.820 -5.791 -0.815 1.00 0.00 ATOM 3 OS2 AOT 151 5.369 -7.134 -0.714 1.00 0.00 ATOM 4 OS3 AOT 151 6.589 -6.277 1.657 1.00 0.00 ATOM 5 C1 AOT 151 7.728 -8.482 0.196 1.00 0.00 ATOM 6 H1 AOT 151 8.702 -8.326 0.676 1.00 0.00 ATOM 7 C2 AOT 151 7.952 -8.937 -1.268 1.00 0.00 ATOM 8 H2 AOT 151 7.067 -9.120 -1.697 1.00 0.00 ATOM 9 H3 AOT 151 8.423 -8.212 -1.771 1.00 0.00 ATOM 10 C3 AOT 151 6.874 -9.526 1.026 1.00 0.00 ATOM 11 O1 AOT 151 6.661 -9.024 2.356 1.00 0.00 ATOM 12 O2 AOT 151 7.505 -10.821 1.169 1.00 0.00 ATOM 13 C4 AOT 151 6.679 -11.663 1.968 1.00 0.00 ATOM 14 H4 AOT 151 5.837 -11.877 1.473 1.00 0.00 ATOM 15 H5 AOT 151 6.454 -11.200
Re: [gmx-users] Re: gmx-users Digest, Vol 114, Issue 15
On 10/28/13 8:07 PM, Hari Pandey wrote: Many thanks to Dr.Lemkul Yes mass is 444 in my .top file and I did -density 1000 because then it will show the density also. If you have one molecule in a box of a known size, you don't need any command-line flags - you have a mass and a known volume. Using -density 1000 is probably harmless, since it is the default, but you can remove that level of complexity in the command (because, again, you are doing things that conflict). I am wandering how do I find that which atom name mismatched. The forcefield folder is in my working directory and there are all files. atomtypes.atp is there and which contains the atom names which I posted last email Hard to say. Your input snippets are incomplete. A rough calculation of the .rtp file gives me a mass of only 375 amu, so I don't know where 444 is coming from and it's impossible to tell if you haven't shown us everything or if there are mistakes somewhere else. -Justin Thanks for your regard Hari On Monday, October 28, 2013 4:50 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/28/13 7:41 PM, Hari Pandey wrote: Thank you so much Mark. I still did not understand. More detaily. Atomtypes are only following: atomtypes.atp:: H 1.00800 ; polar H DUM0.0 ; dummy atom HAL1 1.008000 ; alphatic proton HAL2 1.008000 ; alphatic proton HAL3 1.008000 ; alphatic proton CTL1 12.011000 ;carbonyl C (acetic acid/methyl acetate);;; CTL1 12.011000 ;sp3 carbon with 1 H (-CH1-) CTL2 12.011000 ;carbon of methylene group (-CH2-) CTL3 12.011000 ;carbon of methyl group (-CH3) OBL15.999400 ;acetic acid carboxyl oxygen (e. to protein OB) OCL15.999400 ;acetate oxygen OSL15.999400 ;ester oxygen O2L 15.999400 ;Nucleic acid =O in phosphate or sulfate SL 32.06 ;Sulfate sulfur NA 22.989770; FOR sodium ion MR.rtp: SSL 1.3600 0 OS1O2L-0.60000 OS2O2L-0.60000 OS3O2L-0.60000 C1 CTL1-0.19000 H1 HAL10.0900 0 C2 CTL2-0.18001 H2 HAL20.0900 1 H3 HAL20.0900 1 C3 CL 0.6300 2 ; O1 OBL-0.52002 O2 OSL-0.34002 C4 CTL2-0.18003 H4 HAL20.0900 3 H5 HAL20.0900 3 C5 CTL1-0.09004 H6 HAL10.0900 4 C6 CTL2-0.18005 H7 HAL20.0900 5 H8 HAL20.0900 5 C7 CTL2-0.18006 H9 HAL20.0900 6 H10HAL20.0900 6 C8 CTL2-0.18007 H11HAL20.0900 7 H12HAL20.0900 7 C9 CTL3-0.27008 H13 HAL30.0900 8 H14HAL30.0900 8 H15HAL30.0900 8 C10CTL2-0.18009 H16HAL20.0900 9 H17HAL20.0900 9 C11CTL3-0.270010 H18HAL30.0900 10 H19HAL30.0900 10 H20HAL30.0900 10 C12CL 0.6300 11 ; O3 OBL-0.520011 O4 OSL-0.340011 C13CTL2-0.180012 H21HAL20.0900 12 H22HAL20.0900 12 C14CTL1-0.090013 H23HAL10.0900 13 C15CTL2-0.180014 H24HAL20.0900 14 H25HAL20.0900 14 C16CTL2-0.180015 H26HAL20.0900 15 H27HAL20.0900 15 C17CTL2-0.180016 I have A.pdb and I got A.gro using this force field. Some part of A.pdb:: REMARK Created: Fri Jun 08 12:50:20 Paris, Madrid (heure d'?t?) 2007 CRYST18.760 8.760 8.760 90.00 90.00 90.00 P11 MODEL1 ATOM 1 S AOT 151 6.864 -6.902 0.078 1.00 0.00 ATOM 2 OS1 AOT 151 7.820 -5.791 -0.815 1.00 0.00 ATOM 3 OS2 AOT 151 5.369 -7.134 -0.714 1.00 0.00 ATOM 4 OS3 AOT 151 6.589 -6.277 1.657 1.00 0.00 ATOM 5 C1 AOT 151 7.728 -8.482 0.196 1.00 0.00 ATOM 6 H1 AOT 151 8.702 -8.326 0.676 1.00 0.00
Re: [gmx-users] mdrun cpt
Now /afterok/ might not work since technically the job is killed due to walltime limits - making it not ok. So I suppose /afterany/ is a better option. But I do appreciate your warning about spamming the queue and yes I will re-read PBS docs. On Mon, Oct 28, 2013 at 5:11 PM, Mark Abraham mark.j.abra...@gmail.comwrote: On Mon, Oct 28, 2013 at 7:53 PM, Pavan Ghatty pavan.grom...@gmail.com wrote: Mark, The problem with one .tpr file set for 100ns is that when job number (say) 4 hits the wall limit, it crashes and never gets a chance to submit the next job. So it's not really automated. That's why I suggested -maxh, so you can have an orderly shutdown. (Though if a job can get suspended, that won't always help, because mdrun can't find out about the suspension...) Now I could initiate job 5 before /mdrun/ in job 4's script and hold job 5 till job 4 ends. Sure - read your PBS docs and find the environment variable to read so that job 4 knows its ID so it can submit job 5 with an afterok hold on job 4 on it. But don't tell your sysadmins where I live. ;-) Seriously, if you live on this edge, you could spam infinite jobs, which tends to get your account cut off. That's why you want the afterok hold - you only want the next job to start if the exit code from the first script correctly indicates that mdrun exited correctly. Test carefully! Mark But the PBS queuing system is sometime weird and takes a bit of time to recognize a job and give back its jobID. So I could submit job 5 but be unable to change its status to /hold/ because PBS does not return its ID. Another problem is that if resources are available, job 5 could start before I ever get a chance to /hold/ it. On Mon, Oct 28, 2013 at 11:47 AM, Mark Abraham mark.j.abra...@gmail.com wrote: On Mon, Oct 28, 2013 at 4:27 PM, Pavan Ghatty pavan.grom...@gmail.com wrote: I have need to collect 100ns but I can collect only ~1ns (1000steps) per run. Since I dont have .trr files, I rely on .cpt files for restarts. For example, grompp -f md.mdp -c md_14.gro -t md_14.cpt -p system.top -o md_15 This runs into a problem when the run gets killed due to walltime limits. I now have a .xtc file which has run (say) 700 steps and a .cpt file which was last written at 600th step. You seem to have no need to use grompp, because you don't need to use a workflow that generates multiple .tpr files. Do the equivalent of what the restart page advises: mdrun -s topol.tpr -cpi state.cpt. Thus, make a .tpr for the whole 100ns run, and then keep doing mdrun -s whole-run -cpi whateverwaslast -deffnm whateversuitsyouthistime with or without -append, perhaps with -maxh, keeping whatever manual backups you feel necessary. Then perhaps concatenate your final trajectory files, according to your earlier choices. - To set up the next run I use the .cpt file from 600th step. - Now during analysis if I want to center the protein and such, /trjconv/ needs an .xtc and .tpr file but not a .cpt file. So how does /trjconv/ know to stop at 600th step? trjconv just operates on the contents of the trajectory file, as modified by things like -b -e and -dt. The .tpr just gives it context, such as atom names. You could give it a .tpr from any point during the run. Mark If this has to be put in manually, it becomes cumbersome. Thoughts? On Sun, Oct 27, 2013 at 11:38 AM, Justin Lemkul jalem...@vt.edu wrote: On 10/27/13 9:37 AM, Pavan Ghatty wrote: Hello All, Is there a way to make mdrun put out .cpt file with the same frequency as a .xtc or .trr file. From here http://www.gromacs.org/**Documentation/How-tos/Doing_**Restarts http://www.gromacs.org/Documentation/How-tos/Doing_RestartsI see that we can choose how often (time in mins) the .cpt file is written. But clearly if the frequency of output of .cpt (frequency in mins) and .xtc (frequency in simulation steps) do not match, it can create problems during analysis; especially in the event of frequent crashes. Also, I am not storing .trr file since I dont need that precision. I am using Gromacs 4.6.1. What problems are you experiencing? There is no need for .cpt frequency to be the same as .xtc frequency, because any duplicate frames should be handled elegantly when appending. -Justin -- ==** Justin A. Lemkul, Ph.D. 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 jalemkul@outerbanks.umaryland.**edu
[gmx-users] lmc-stats
When performing free energy calculations using the expanded ensemble method, there is a barker and metropolis option for lmc-stats. Are the corresponding transition probabilities computed with or without the weighting factors? That is, are these probabilities biased or not? Thank you, Andrew -- Andrew S. Paluch, PhD Department of Chemical, Paper, and Biomedical Engineering Miami University paluc...@miamioh.edu (513) 529-0784 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] lmc-stats
Hi, Andrew- The choice of lmc-stats only affects the calculation of the weights, it does not affect the calculation of the transition matrix. There are two possibilities for the transition matrix; the estimated one (which is just called 'Transition Matrix' -- we should probably have a better name), and the empirical one. The empirical transition matrix is just transition counts. The first one is an ensemble average of P(k|x); for neighbor moves, this is just the average of the barker transition probabilities (plus the choice of going up or down), Let me know if this is useful. Not that many people have used this code, thus there are likely ways that it can be improved for better utility. I generally haven't tried to calculate free energy differences from the transition matrix, though it should give consistent results with the other methods. Best, Michael Shirts Assistant Professor Department of Chemical Engineering University of Virginia michael.shi...@virginia.edu (434)-243-1821 On Mon, Oct 28, 2013 at 11:13 PM, Andrew S. Paluch paluc...@miamioh.edu wrote: When performing free energy calculations using the expanded ensemble method, there is a barker and metropolis option for lmc-stats. Are the corresponding transition probabilities computed with or without the weighting factors? That is, are these probabilities biased or not? Thank you, Andrew -- Andrew S. Paluch, PhD Department of Chemical, Paper, and Biomedical Engineering Miami University paluc...@miamioh.edu (513) 529-0784 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
