[gmx-users] free energy
Dear Kieu Thu Thanks for your comment about free energy. Unfortunately, I could not send a email to Paissoni Cristina in the Gromacs Forum. Could you give me email address of Paissoni Cristina? Finding a tool for calculation MM/PBSA with Gromacs is very vital for me. Best Regards 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
[gmx-users] Reproducing results with independent runs
Dear users, I am investigating protein crystal packing artifacts by doing equilibrium simulations starting from a crystal structure. I would like to know if the relaxations i see are reproducible, in the sense that many simulations with independent velocities give the same general result. My plans is to do only one set of (first NVT then NPT) equilibrations with position restraints. Then, I thought I'd do a shorter NPT run with position restraints, with more frequent output and using the trr snapshots as starting points for production runs. The only question then is how far apart these snapshots need to be to guarantee independent velocities. Attached is the velocity autocorrelation for the Protein group. It seems to me that using snapshots 1ps apart would do it, since the autocorrelation has decayed by then. Is this a valid approach? Best, Alex http://gromacs.5086.x6.nabble.com/file/n5012372/vac.png -- View this message in context: http://gromacs.5086.x6.nabble.com/Reproducing-results-with-independent-runs-tp5012372.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] Trouble calculating MSD after removing COM for upper and lower leaflets
Hi All, I have a few older membrane simulations for which the COM for the upper and lower leaflets were not removed in the course of the simulations. These are pretty long simulations exceeding 300 ns. I have trouble with post-processing of the trajectory. To remove the COM of the upper and lower leaflets separately, I executed the following series of commands (shown for upper only): Selecting upper leaflet: g_select -s .tpr -on upper_P8.ndx -select 'resname DPPC and name P8 and res_com z4.3' trjconv -f .gro -s .gro -n upper_P8.ndx -o test_u_P8.pdb .Testing selection, everthing ok Trajectory: trjconv -f .xtc -s .tpr -n upper_P8.ndx -o upperP8_center_pbcnojump.xtc -center -b 2 -pbc nojump MSD: g_msd -f upperP8_center_pbcnojump.xtc -s .tpr -o msd_dppc_x_u.xvg -type x -n upper_P8.ndx Select a group to calculate mean squared displacement for: Group 0 (resname_DPPC_and_name_P8_and_res_com_z4.3_0.000) has 192 elements There is one group in the index Reading frame 60 time 20600.000 Segmentation fault (core dumped) Any ideas? Is there anything wrong with my workflow? Thanks. -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- 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] Umbrella Sampling tutorial
Daer Justin I studied your tutorial (Umbrella Sampling). It is very beneficial for me. The system you considered was the dissociation of a single peptide from the growing end of an protofibril. You considered following parameters: Chain_B: reference group for pulling. Chain_A: group to which pulling force is applied. pulling direction was Z. you placed the center of mass of the protofibril at (3.280, 2.181, 2.4775) in a box of dimensions 6.560 x 4.362 x 12 by editconf: editconf -f complex.gro -o newbox.gro -center 3.280 2.181 2.4775 -box 6.560 4.362 12. I have a question: You said pull distance must always be less than one-half the length of the box vector along which the pulling is being conducted.You pulled a total distance of 5.0 nm in a 12.0-nm box, to avoid the complications described above. Why did you used 2.4775? I think 5.0 is true. Please give me more explanation. How did you obtained this value? Best wishes -- 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: choosing force field
On 11/9/13 12:48 AM, pratibha wrote: Sorry for the previous mistake. Instead of 53a7, the force field which I used was 53a6. 53A6 is known to under-stabilize helices, so if a helix did not appear in a simulation using this force field, it is not definitive proof that the structure does not populate helical structures. I generally see mixed opinions in the literature in terms of which Gromos parameter set is the most reliable. As was asked by someone else, is there a reason you are only considering Gromos parameter sets? Others may be better suited to your study. -Justin On Fri, Nov 8, 2013 at 12:10 AM, Justin Lemkul [via GROMACS] ml-node+s5086n5012325...@n6.nabble.com wrote: On 11/7/13 12:14 PM, pratibha wrote: My protein contains metal ions which are parameterized only in gromos force field. Since I am a newbie to MD simulations, it would be difficult for me to parameterize those myself. Can you please guide me as per my previous mail which out of the two simulations should I consider more reliable-43a1 or 53a7? AFAIK, there is no such thing as 53A7, and your original message was full of similar typos, making it nearly impossible to figure out what you were actually doing. Can you indicate the actual force field(s) that you have been using in case someone has any ideas? The difference between 53A6 and 54A7 should be quite pronounced, in my experience, thus any guesses as to what 53A7 should be doing are not productive because I don't know what that is. -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 [hidden email] http://user/SendEmail.jtp?type=nodenode=5012325i=0 | (410) 706-7441 == -- gmx-users mailing list[hidden email]http://user/SendEmail.jtp?type=nodenode=5012325i=1 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 [hidden email]http://user/SendEmail.jtp?type=nodenode=5012325i=2. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- If you reply to this email, your message will be added to the discussion below: http://gromacs.5086.x6.nabble.com/choosing-force-field-tp5012242p5012325.html To unsubscribe from choosing force field, click herehttp://gromacs.5086.x6.nabble.com/template/NamlServlet.jtp?macro=unsubscribe_by_codenode=5012242code=a2Fwb29ycHJhdGliaGE3QGdtYWlsLmNvbXw1MDEyMjQyfC02NjkwNjY5MjU= . NAMLhttp://gromacs.5086.x6.nabble.com/template/NamlServlet.jtp?macro=macro_viewerid=instant_html%21nabble%3Aemail.namlbase=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespacebreadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml -- View this message in context: http://gromacs.5086.x6.nabble.com/choosing-force-field-tp5012242p5012370.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- == 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] Trouble calculating MSD after removing COM for upper and lower leaflets
On 11/9/13 5:24 AM, rajat desikan wrote: Hi All, I have a few older membrane simulations for which the COM for the upper and lower leaflets were not removed in the course of the simulations. These are pretty long simulations exceeding 300 ns. I have trouble with post-processing of the trajectory. To remove the COM of the upper and lower leaflets separately, I executed the following series of commands (shown for upper only): Selecting upper leaflet: g_select -s .tpr -on upper_P8.ndx -select 'resname DPPC and name P8 and res_com z4.3' trjconv -f .gro -s .gro -n upper_P8.ndx -o test_u_P8.pdb .Testing selection, everthing ok Trajectory: trjconv -f .xtc -s .tpr -n upper_P8.ndx -o upperP8_center_pbcnojump.xtc -center -b 2 -pbc nojump MSD: g_msd -f upperP8_center_pbcnojump.xtc -s .tpr -o msd_dppc_x_u.xvg -type x -n upper_P8.ndx You probably want the -lateral option as well. Select a group to calculate mean squared displacement for: Group 0 (resname_DPPC_and_name_P8_and_res_com_z4.3_0.000) has 192 elements Does the fact that there are 192 identified P8 atoms match your expectations for this membrane? -Justin There is one group in the index Reading frame 60 time 20600.000 Segmentation fault (core dumped) Any ideas? Is there anything wrong with my workflow? Thanks. -- == 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] Umbrella Sampling tutorial
On 11/9/13 8:22 AM, shahab shariati wrote: Daer Justin I studied your tutorial (Umbrella Sampling). It is very beneficial for me. The system you considered was the dissociation of a single peptide from the growing end of an protofibril. You considered following parameters: Chain_B: reference group for pulling. Chain_A: group to which pulling force is applied. pulling direction was Z. you placed the center of mass of the protofibril at (3.280, 2.181, 2.4775) in a box of dimensions 6.560 x 4.362 x 12 by editconf: editconf -f complex.gro -o newbox.gro -center 3.280 2.181 2.4775 -box 6.560 4.362 12. I have a question: You said pull distance must always be less than one-half the length of the box vector along which the pulling is being conducted.You pulled a total distance of 5.0 nm in a 12.0-nm box, to avoid the complications described above. Why did you used 2.4775? I think 5.0 is true. Please give me more explanation. How did you obtained this value? I knew I needed a rectangular box, given the intrinsic geometry of the protein complex and the manner in which I was pulling, so I started by building a cubic box around the pentamer that satisfied normal minimum image convention criteria based on my cutoffs. I noted its dimensions and extended the box by 5.0 nm along z, then added a bit of padding space, because the COM distance itself is not the only factor that is important; I had to simultaneously account for the fact that I was unfolding a peptide along the reaction coordinate. So I added a bit more space for good measure to avoid spurious PBC interactions at the end of the reaction coordinate. It's all fairly empirical, determined stepwise by accounting for the important features of the system. -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] Simulation box size, LIE and PME
On 11/8/13 2:27 PM, Williams Ernesto Miranda Delgado wrote: Greetings The discussion list had helped me about understanding what to do when I want to calculate binding free energy using LIE after doing MD simulation using PME. Now I need your help about choosing the simulation box size for ligand and complex. I used -d 1.0 in editconf for the complex simulation and -d 1.6 for the ligand simulation. Are this values ok? Should I use a different value of -d for the ligand simulation? The value of -d should be set based on the cutoffs used in the simulation (inherent to the chosen force field) to avoid minimum image convention violations. Depending on the size of the ligand, you may just want to set the box size manually with editconf -box. -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: Ligand simulation for LIE with PME
On 11/8/13 3:32 PM, Williams Ernesto Miranda Delgado wrote: Greetings again If I use a salt concentration for neutralizing the protein-ligand complex and run MD using PME, and the ligand is neutral, do I perform ligand MD simulation without adding any salt concentration? It could be relevant for LIE free energy calculation if I don't include salt in ligand (neutral) simulation, even when I simulate Protein-ligand system with salt? My assumption would be that you should introduce as few differences as possible. Consider what LIE is doing - it is attempting to estimate the free energy of binding from simple interaction energies. If you determine the strength of the ligand-protein interaction in the presence of some higher ionic strength medium, and then determine only the strength of ligand-water interactions rather than the interaction of the ligand with the same medium, then I'd say the calculation is flawed. Think of what is really happening in real life - the ligand has to partition out of the solvent and into the protein's binding site. The solvent is uniform throughout that process. -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] Umbrella Sampling tutorial
Dear Justin Thanks for your explanation. My system contains lipid bilayer + drug + water molecules. I want to calculate Potential of mean force as a function of the distance between the centers of mass of drug and the lipid bilayer. Box vector along which the pulling is being conducted is Z. 1) Are these issues true about my system? lipid bilayer = reference group for pulling. drug molecule = group to which pulling force is applied. Then, should I use position restraining on the lipid bilayer? 2) The system you considered was the dissociation of a single peptide from the growing end of an protofibril. So, in your summary_distances.dat, distance between chain A and chain B was increased. But, I want to consider translocation of the drug molecule from water into the lipid bilayer. On the other hand, I want to consider approaching drug molecule to lipid bilayer. So, in my summary_distances.dat, distance between drug molecule and lipid bilayer will be decrease. My mean is that my case is contrary to your case. Nonetheless, should I use exactly Pull code section of your md_pull.mdp file? Best wishes -- 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] Umbrella Sampling tutorial
On 11/9/13 9:38 AM, shahab shariati wrote: Dear Justin Thanks for your explanation. My system contains lipid bilayer + drug + water molecules. I want to calculate Potential of mean force as a function of the distance between the centers of mass of drug and the lipid bilayer. Box vector along which the pulling is being conducted is Z. 1) Are these issues true about my system? lipid bilayer = reference group for pulling. drug molecule = group to which pulling force is applied. Then, should I use position restraining on the lipid bilayer? I see no reason for that. The use of position restraints represents a special case, the logic for which is described in our paper. Please do not extrapolate too literally from my tutorial to your system. 2) The system you considered was the dissociation of a single peptide from the growing end of an protofibril. So, in your summary_distances.dat, distance between chain A and chain B was increased. But, I want to consider translocation of the drug molecule from water into the lipid bilayer. On the other hand, I want to consider approaching drug molecule to lipid bilayer. So, in my summary_distances.dat, distance between drug molecule and lipid bilayer will be decrease. ...and then increase, if you want to study the partitioning across the membrane. My mean is that my case is contrary to your case. Nonetheless, should I use exactly Pull code section of your md_pull.mdp file? Absolutely not! Please refer to the advanced section of the tutorial. The settings you will need will be very different from the tutorial, which represents the simplest possible case of pulling. -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] Trouble calculating MSD after removing COM for upper and lower leaflets
Hi Justin, 1) I am doing all three. -type x, -type y, -lateral z (xy) ...(I am looking at anisotropy in dynamics if any) 2) Yes, 192 phosphate beads is exact. I have 384 lipids in my system (192/leaflet) If you were to remove the COM motion of individual leaflets and extract the MSD, what would you do? Do you see any error in my workflow? Thanks. Appreciate any suggestions... On Sat, Nov 9, 2013 at 7:16 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/9/13 5:24 AM, rajat desikan wrote: Hi All, I have a few older membrane simulations for which the COM for the upper and lower leaflets were not removed in the course of the simulations. These are pretty long simulations exceeding 300 ns. I have trouble with post-processing of the trajectory. To remove the COM of the upper and lower leaflets separately, I executed the following series of commands (shown for upper only): Selecting upper leaflet: g_select -s .tpr -on upper_P8.ndx -select 'resname DPPC and name P8 and res_com z4.3' trjconv -f .gro -s .gro -n upper_P8.ndx -o test_u_P8.pdb .Testing selection, everthing ok Trajectory: trjconv -f .xtc -s .tpr -n upper_P8.ndx -o upperP8_center_pbcnojump.xtc -center -b 2 -pbc nojump MSD: g_msd -f upperP8_center_pbcnojump.xtc -s .tpr -o msd_dppc_x_u.xvg -type x -n upper_P8.ndx You probably want the -lateral option as well. Select a group to calculate mean squared displacement for: Group 0 (resname_DPPC_and_name_P8_and_res_com_z4.3_0.000) has 192 elements Does the fact that there are 192 identified P8 atoms match your expectations for this membrane? -Justin There is one group in the index Reading frame 60 time 20600.000 Segmentation fault (core dumped) Any ideas? Is there anything wrong with my workflow? Thanks. -- == 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 -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- 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] Trouble calculating MSD after removing COM for upper and lower leaflets
On 11/9/13 11:37 AM, rajat desikan wrote: Hi Justin, 1) I am doing all three. -type x, -type y, -lateral z (xy) ...(I am looking at anisotropy in dynamics if any) 2) Yes, 192 phosphate beads is exact. I have 384 lipids in my system (192/leaflet) If you were to remove the COM motion of individual leaflets and extract the MSD, what would you do? Do you see any error in my workflow? Thanks. Appreciate any suggestions... What you did looks reasonable to me. Seg faults are frustrating, but can only really be addressed by recompiling in debug mode and running the command through a debugger to see which function is failing. -Justin On Sat, Nov 9, 2013 at 7:16 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/9/13 5:24 AM, rajat desikan wrote: Hi All, I have a few older membrane simulations for which the COM for the upper and lower leaflets were not removed in the course of the simulations. These are pretty long simulations exceeding 300 ns. I have trouble with post-processing of the trajectory. To remove the COM of the upper and lower leaflets separately, I executed the following series of commands (shown for upper only): Selecting upper leaflet: g_select -s .tpr -on upper_P8.ndx -select 'resname DPPC and name P8 and res_com z4.3' trjconv -f .gro -s .gro -n upper_P8.ndx -o test_u_P8.pdb .Testing selection, everthing ok Trajectory: trjconv -f .xtc -s .tpr -n upper_P8.ndx -o upperP8_center_pbcnojump.xtc -center -b 2 -pbc nojump MSD: g_msd -f upperP8_center_pbcnojump.xtc -s .tpr -o msd_dppc_x_u.xvg -type x -n upper_P8.ndx You probably want the -lateral option as well. Select a group to calculate mean squared displacement for: Group 0 (resname_DPPC_and_name_P8_and_res_com_z4.3_0.000) has 192 elements Does the fact that there are 192 identified P8 atoms match your expectations for this membrane? -Justin There is one group in the index Reading frame 60 time 20600.000 Segmentation fault (core dumped) Any ideas? Is there anything wrong with my workflow? Thanks. -- == 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 -- == 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] Trouble calculating MSD after removing COM for upper and lower leaflets
Hi Justin, Thanks for your time. I think I will use g_traj to spit out the P8 coordinates from upperP8_center_pbcnojump.xtc and write my own little MSD routine :) On Sat, Nov 9, 2013 at 11:36 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/9/13 11:37 AM, rajat desikan wrote: Hi Justin, 1) I am doing all three. -type x, -type y, -lateral z (xy) ...(I am looking at anisotropy in dynamics if any) 2) Yes, 192 phosphate beads is exact. I have 384 lipids in my system (192/leaflet) If you were to remove the COM motion of individual leaflets and extract the MSD, what would you do? Do you see any error in my workflow? Thanks. Appreciate any suggestions... What you did looks reasonable to me. Seg faults are frustrating, but can only really be addressed by recompiling in debug mode and running the command through a debugger to see which function is failing. -Justin On Sat, Nov 9, 2013 at 7:16 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/9/13 5:24 AM, rajat desikan wrote: Hi All, I have a few older membrane simulations for which the COM for the upper and lower leaflets were not removed in the course of the simulations. These are pretty long simulations exceeding 300 ns. I have trouble with post-processing of the trajectory. To remove the COM of the upper and lower leaflets separately, I executed the following series of commands (shown for upper only): Selecting upper leaflet: g_select -s .tpr -on upper_P8.ndx -select 'resname DPPC and name P8 and res_com z4.3' trjconv -f .gro -s .gro -n upper_P8.ndx -o test_u_P8.pdb .Testing selection, everthing ok Trajectory: trjconv -f .xtc -s .tpr -n upper_P8.ndx -o upperP8_center_pbcnojump.xtc -center -b 2 -pbc nojump MSD: g_msd -f upperP8_center_pbcnojump.xtc -s .tpr -o msd_dppc_x_u.xvg -type x -n upper_P8.ndx You probably want the -lateral option as well. Select a group to calculate mean squared displacement for: Group 0 (resname_DPPC_and_name_P8_and_res_com_z4.3_0.000) has 192 elements Does the fact that there are 192 identified P8 atoms match your expectations for this membrane? -Justin There is one group in the index Reading frame 60 time 20600.000 Segmentation fault (core dumped) Any ideas? Is there anything wrong with my workflow? Thanks. -- == 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 -- == 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 -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- 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] Reproducing results with independent runs
On Sat, Nov 9, 2013 at 9:36 AM, alex.bjorling alex.bjorl...@gmail.comwrote: Dear users, I am investigating protein crystal packing artifacts by doing equilibrium simulations starting from a crystal structure. I would like to know if the relaxations i see are reproducible, in the sense that many simulations with independent velocities give the same general result. My plans is to do only one set of (first NVT then NPT) equilibrations with position restraints. Then, I thought I'd do a shorter NPT run with position restraints, with more frequent output and using the trr snapshots as starting points for production runs. The only question then is how far apart these snapshots need to be to guarantee independent velocities. Attached is the velocity autocorrelation for the Protein group. It seems to me that using snapshots 1ps apart would do it, since the autocorrelation has decayed by then. Is this a valid approach? That the observations are uncorrelated (because the autocorrelation time has elapsed) does not imply that trajectories started from successive snapshots would be independent - in the absence of floating-point or load-balancing artefacts leading to numerical divergence, the separate simulations would nearly reproduce each other! Since you have to wait for a period of divergence anyway, you might as well generate new velocities after an initial stage of equilibration, equilibrate further, and have no independence question to answer. Mark -- 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] Re: CHARMM .mdp settings for GPU
Hi Justin, I take it that both the sets of parameters should produce identical macroscopic quantities. For the GPU, is this a decent .mdp? cutoff-scheme= Verlet vdwtype = switch rlist= 1.2 ;rlistlong = 1.4 NOT USED IN GPU...IS THIS OK? rvdw = 1.2 ;rvdw-switch= 1.0NOT USED IN GPU...IS THIS OK? coulombtype = pme DispCorr = EnerPres rcoulomb= 1.2 On Fri, Nov 8, 2013 at 7:19 PM, Justin Lemkul [via GROMACS] ml-node+s5086n5012351...@n6.nabble.com wrote: On 11/7/13 11:32 PM, Rajat Desikan wrote: Dear All, The setting that I mentioned above are from Klauda et al., for a POPE membrane system. They can be found in charmm_npt.mdp in lipidbook (link below) http://lipidbook.bioch.ox.ac.uk/package/show/id/48.html Is there any reason not to use their .mdp parameters for a membrane-protein system? Justin's recommendation is highly valued since I am using his forcefield. Justin, your comments please Careful now, it's not my forcefield. I derived only a very small part of it :) To summarize: Klauda et al., suggest rlist = 1.0 rlistlong= 1.4 rvdw_switch = 0.8 vdwtype= Switch coulombtype = pme DispCorr= EnerPres ;only usefull with reaction-field and pme or pppm rcoulomb = 1.0 rcoulomb_switch= 0.0 rvdw = 1.2 Justin's recommendation (per mail above) vdwtype = switch rlist = 1.2 rlistlong = 1.4 rvdw = 1.2 rvdw-switch = 1.0 rcoulomb = 1.2 The differences between these two sets of run parameters are very small, dealing mostly with Coulomb and neighbor searching cutoffs. I would suspect that any difference between simulations run with these two settings would be similarly small or nonexistent, given that rcoulomb is a bit flexible when using PME. The value of rlist is rarely mentioned in papers, so it is good that the authors have provided the actual input file. Previous interpretation of CHARMM usage generally advised setting rcoulomb = 1.2 to remain consistent with the original switching/shifting functions. That setting becomes a bit less stringent when using PME. -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 [hidden email] http://user/SendEmail.jtp?type=nodenode=5012351i=0 | (410) 706-7441 == -- gmx-users mailing list[hidden email]http://user/SendEmail.jtp?type=nodenode=5012351i=1 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 [hidden email]http://user/SendEmail.jtp?type=nodenode=5012351i=2. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- If you reply to this email, your message will be added to the discussion below: http://gromacs.5086.x6.nabble.com/CHARMM-mdp-settings-for-GPU-tp5012267p5012351.html To unsubscribe from CHARMM .mdp settings for GPU, click herehttp://gromacs.5086.x6.nabble.com/template/NamlServlet.jtp?macro=unsubscribe_by_codenode=5012267code=cmFqYXRkZXNpa2FuQGdtYWlsLmNvbXw1MDEyMjY3fDM0NzUwNzcwNA== . NAMLhttp://gromacs.5086.x6.nabble.com/template/NamlServlet.jtp?macro=macro_viewerid=instant_html%21nabble%3Aemail.namlbase=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespacebreadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- 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: CHARMM .mdp settings for GPU
On 11/9/13 4:16 PM, rajat desikan wrote: Hi Justin, I take it that both the sets of parameters should produce identical macroscopic quantities. For the GPU, is this a decent .mdp? cutoff-scheme= Verlet vdwtype = switch rlist= 1.2 ;rlistlong = 1.4 NOT USED IN GPU...IS THIS OK? rvdw = 1.2 ;rvdw-switch= 1.0NOT USED IN GPU...IS THIS OK? coulombtype = pme DispCorr = EnerPres rcoulomb= 1.2 I have no basis for saying whether or not it will produce correct results. I have never tested this force field on GPU with the Verlet scheme. My biggest concern is with the treatment of van der Waals interactions, and I have not used the Verlet scheme enough to understand what it is doing and how it will treat the interactions that should be switched. If someone else can comment, that would be useful to me, as well! Test carefully and please report back. A comparison between CPU and GPU would be very valuable. -Justin On Fri, Nov 8, 2013 at 7:19 PM, Justin Lemkul [via GROMACS] ml-node+s5086n5012351...@n6.nabble.com wrote: On 11/7/13 11:32 PM, Rajat Desikan wrote: Dear All, The setting that I mentioned above are from Klauda et al., for a POPE membrane system. They can be found in charmm_npt.mdp in lipidbook (link below) http://lipidbook.bioch.ox.ac.uk/package/show/id/48.html Is there any reason not to use their .mdp parameters for a membrane-protein system? Justin's recommendation is highly valued since I am using his forcefield. Justin, your comments please Careful now, it's not my forcefield. I derived only a very small part of it :) To summarize: Klauda et al., suggest rlist = 1.0 rlistlong= 1.4 rvdw_switch = 0.8 vdwtype= Switch coulombtype = pme DispCorr= EnerPres ;only usefull with reaction-field and pme or pppm rcoulomb = 1.0 rcoulomb_switch= 0.0 rvdw = 1.2 Justin's recommendation (per mail above) vdwtype = switch rlist = 1.2 rlistlong = 1.4 rvdw = 1.2 rvdw-switch = 1.0 rcoulomb = 1.2 The differences between these two sets of run parameters are very small, dealing mostly with Coulomb and neighbor searching cutoffs. I would suspect that any difference between simulations run with these two settings would be similarly small or nonexistent, given that rcoulomb is a bit flexible when using PME. The value of rlist is rarely mentioned in papers, so it is good that the authors have provided the actual input file. Previous interpretation of CHARMM usage generally advised setting rcoulomb = 1.2 to remain consistent with the original switching/shifting functions. That setting becomes a bit less stringent when using PME. -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 [hidden email] http://user/SendEmail.jtp?type=nodenode=5012351i=0 | (410) 706-7441 == -- gmx-users mailing list[hidden email]http://user/SendEmail.jtp?type=nodenode=5012351i=1 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 [hidden email]http://user/SendEmail.jtp?type=nodenode=5012351i=2. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- If you reply to this email, your message will be added to the discussion below: http://gromacs.5086.x6.nabble.com/CHARMM-mdp-settings-for-GPU-tp5012267p5012351.html To unsubscribe from CHARMM .mdp settings for GPU, click herehttp://gromacs.5086.x6.nabble.com/template/NamlServlet.jtp?macro=unsubscribe_by_codenode=5012267code=cmFqYXRkZXNpa2FuQGdtYWlsLmNvbXw1MDEyMjY3fDM0NzUwNzcwNA== . NAMLhttp://gromacs.5086.x6.nabble.com/template/NamlServlet.jtp?macro=macro_viewerid=instant_html%21nabble%3Aemail.namlbase=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespacebreadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml -- == 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
[gmx-users] Re: CHARMM .mdp settings for GPU
On Sat, 9 Nov 2013, Gianluca Interlandi wrote: Just to chime in. Here is a that paper might be helpful in understanding the role of cuoffs in the CHARMM force field: AU STEINBACH, PJ BROOKS, BR AF STEINBACH, PJ BROOKS, BR TI NEW SPHERICAL-CUTOFF METHODS FOR LONG-RANGE FORCES IN MACROMOLECULAR SIMULATION SO JOURNAL OF COMPUTATIONAL CHEMISTRY SN 0192-8651 PD JUL PY 1994 VL 15 IS 7 BP 667 EP 683 DI 10.1002/jcc.540150702 UT WOS:A1994NU1741 Gianluca On Sat, 9 Nov 2013, Justin Lemkul wrote: On 11/9/13 4:16 PM, rajat desikan wrote: Hi Justin, I take it that both the sets of parameters should produce identical macroscopic quantities. For the GPU, is this a decent .mdp? cutoff-scheme= Verlet vdwtype = switch rlist= 1.2 ;rlistlong = 1.4 NOT USED IN GPU...IS THIS OK? rvdw = 1.2 ;rvdw-switch= 1.0NOT USED IN GPU...IS THIS OK? coulombtype = pme DispCorr = EnerPres rcoulomb= 1.2 I have no basis for saying whether or not it will produce correct results. I have never tested this force field on GPU with the Verlet scheme. My biggest concern is with the treatment of van der Waals interactions, and I have not used the Verlet scheme enough to understand what it is doing and how it will treat the interactions that should be switched. If someone else can comment, that would be useful to me, as well! Test carefully and please report back. A comparison between CPU and GPU would be very valuable. -Justin On Fri, Nov 8, 2013 at 7:19 PM, Justin Lemkul [via GROMACS] ml-node+s5086n5012351...@n6.nabble.com wrote: On 11/7/13 11:32 PM, Rajat Desikan wrote: Dear All, The setting that I mentioned above are from Klauda et al., for a POPE membrane system. They can be found in charmm_npt.mdp in lipidbook (link below) http://lipidbook.bioch.ox.ac.uk/package/show/id/48.html Is there any reason not to use their .mdp parameters for a membrane-protein system? Justin's recommendation is highly valued since I am using his forcefield. Justin, your comments please Careful now, it's not my forcefield. I derived only a very small part of it :) To summarize: Klauda et al., suggest rlist = 1.0 rlistlong= 1.4 rvdw_switch = 0.8 vdwtype= Switch coulombtype = pme DispCorr= EnerPres ;only usefull with reaction-field and pme or pppm rcoulomb = 1.0 rcoulomb_switch= 0.0 rvdw = 1.2 Justin's recommendation (per mail above) vdwtype = switch rlist = 1.2 rlistlong = 1.4 rvdw = 1.2 rvdw-switch = 1.0 rcoulomb = 1.2 The differences between these two sets of run parameters are very small, dealing mostly with Coulomb and neighbor searching cutoffs. I would suspect that any difference between simulations run with these two settings would be similarly small or nonexistent, given that rcoulomb is a bit flexible when using PME. The value of rlist is rarely mentioned in papers, so it is good that the authors have provided the actual input file. Previous interpretation of CHARMM usage generally advised setting rcoulomb = 1.2 to remain consistent with the original switching/shifting functions. That setting becomes a bit less stringent when using PME. -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 [hidden email] http://user/SendEmail.jtp?type=nodenode=5012351i=0 | (410) 706-7441 == -- gmx-users mailing list[hidden email]http://user/SendEmail.jtp?type=nodenode=5012351i=1 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 [hidden email]http://user/SendEmail.jtp?type=nodenode=5012351i=2. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- If you reply to this email, your message will be added to the discussion below: http://gromacs.5086.x6.nabble.com/CHARMM-mdp-settings-for-GPU-tp5012267p5012351.html To unsubscribe from CHARMM .mdp settings for GPU, click herehttp://gromacs.5086.x6.nabble.com/template/NamlServlet.jtp?macro=unsubscribe_by_codenode=5012267code=cmFqYXRkZXNpa2FuQGdtYWlsLmNvbXw1MDEyMjY3fDM0NzUwNzcwNA== .
Re: [gmx-users] Re: CHARMM .mdp settings for GPU
On 11/9/13 9:51 PM, Gianluca Interlandi wrote: On Sat, 9 Nov 2013, Gianluca Interlandi wrote: Just to chime in. Here is a that paper might be helpful in understanding the role of cuoffs in the CHARMM force field: AU STEINBACH, PJ BROOKS, BR AF STEINBACH, PJ BROOKS, BR TI NEW SPHERICAL-CUTOFF METHODS FOR LONG-RANGE FORCES IN MACROMOLECULAR SIMULATION SO JOURNAL OF COMPUTATIONAL CHEMISTRY SN 0192-8651 PD JUL PY 1994 VL 15 IS 7 BP 667 EP 683 DI 10.1002/jcc.540150702 UT WOS:A1994NU1741 Yes, that's the one I posted several weeks back. It describes the original implementation of cutoff schemes in CHARMM. -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: mdrun on 8-core AMD + GTX TITAN (was: Re: [gmx-users] Re: Gromacs-4.6 on two Titans GPUs)
Hi Szilard, Thank you very much for your suggestions. Actually, I was jumping to conclusions too early, as you mentioned AMD cluster, I assumed you must have 12-16-core Opteron CPUs. If you have an 8-core (desktop?) AMD CPU, than you may not need to run more than one rank per GPU. Yes, we do have independent clusters of AMD, AMD opteron, Intel Corei7. All nodes of three clusters are installed with (at least) 1 GPU card. I have run the same test on these three clusters. Let's focus on a basic scaling issue: One GPU v.s Two GPUs within the same node of 8-core AMD cpu. Using 1 GPU, we can have a performance of ~32 ns/day. Using two GPU, we gain not much more ( ~38.5 ns/day ). It is about ~20% more performance. However, this is not really true because in some tests, I also saw only 2-5% more, which really surprised me. As you can see, this test was made on the same node regardless of networking. Can the performance be improved say 50% more when 2 GPUs are used on a general task ? If yes, how ? Indeed, as Richard pointed out, I was asking for *full* logs, these summaries can't tell much, the table above the summary entitled R E A L C Y C L E A N D T I M E A C C O U N T I N G as well as other reported information across the log file is what I need to make an assessment of your simulations' performance. Please see below. However, in your case I suspect that the bottleneck is multi-threaded scaling on the AMD CPUs and you should probably decrease the number of threads per MPI rank and share GPUs between 2-4 ranks. After I test all three clusters, I found it may NOT be an issue of AMD cpus. Intel cpus has the SAME scaling issue. However, I am curious as to how you justify the setup of 2-4 ranks sharing GPUs ? Can you please explain it a bit more ? You could try running mpirun -np 4 mdrun -ntomp 2 -gpu_id 0011 but I suspect this won't help because your scaling issue Your guess is correct but why is that ? it is worse. The more nodes are involved in a task, the performance is worse. in my experience even reaction field runs don't scale across nodes with 10G ethernet if you have more than 4-6 ranks per node trying to communicate (let alone with PME). What dose it mean let alone with PME ? how to do so ? by mdrun ? I do know mdrun -npme to specify PME process. Thank you. Dwey ### One GPU R E A L C Y C L E A N D T I M E A C C O U N T I N G Computing: Nodes Th. Count Wall t (s) G-Cycles % - Neighbor search18 11 431.81713863.390 1.6 Launch GPU ops.18501 472.90615182.556 1.7 Force 185011328.61142654.785 4.9 PME mesh 18501 11561.327 371174.09042.8 Wait GPU local 185016888.008 221138.11125.5 NB X/F buffer ops. 189911216.49939055.455 4.5 Write traj.18 1030 12.741 409.039 0.0 Update 185011696.35854461.226 6.3 Constraints185011969.72663237.647 7.3 Rest 11458.82046835.133 5.4 - Total 1 27036.812 868011.431 100.0 - - PME spread/gather 18 10026975.086 223933.73925.8 PME 3D-FFT 18 10023928.259 126115.97614.5 PME solve 18501 636.48820434.327 2.4 - GPU timings - Computing: Count Wall t (s) ms/step % - Pair list H2D 11 43.4350.434 0.2 X / q H2D501 567.1680.113 2.8 Nonbonded F kernel 400 14174.3163.54470.8 Nonbonded F+ene k.904314.4384.79421.5 Nonbonded F+ene+prune k. 11 572.3705.724 2.9 F D2H501 358.1200.072 1.8 - Total 20029.8464.006 100.0 - Force evaluation time GPU/CPU: 4.006 ms/2.578 ms = 1.554 For optimal performance this ratio should be close to 1!
[gmx-users] Re: g_analyze
Hi, I used the command g_hbond to find h-bond between residues 115-118 and water. Then I used g_analyze to find out the average and it gives the value for the hbonds like this :- std. dev.relative deviation of standard - cumulants from those of set average deviation sqrt(n-1) a Gaussian distribition cum. 3 cum. 4 SS1 6.877249e-02 2.546419e-01 5.092839e-03 2.1813.495 SS2 6.997201e-02 2.673450e-01 5.346901e-03 2.4215.001 When I calculated the average manually, by taking the average of numbers in second column of hbnum.xvg file, I got a value of around 13.5.. What is the reason for such a large difference. In another case, g_analyze gives avg values of aroun 6.9 for hbond between two residues and when I calculated it maually I got the avg values as 6.8 .. Whats the meaning of SS1 and SS2,?? Does it mean that SS1 refers to time and SS2 refers to hbond numbers in the hbnum.xvg obtained from g_hbond analysis ?? Please clarify these doubts.. Regards Bharat -- 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] About Compiler Compatibility for Gromacs 4.6.2 Compilation
Dear Justin and Mark Thank you for your Previous reply Can i Use the Following Intel Compiler for grmacs 4.6.2 in centos Linux OS ? Intel® C++ Composer XE 2013 for Linux it Includes Intel® C++ Compiler, Intel® Integrated Performance Primitives 7.1, Intel® Math Kernel Library 11.0, Intel Cilk™ Plus, the Intel® Threading Building Blocks (Intel® TBB)” -- 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
