[gmx-users] minimization for final configuration
hi GMX users i have simulated the protein-ligand complex by gromacs for 20ns. The average for the final structure of 18 to 20 nanoseconds has been achieved.is minimization for the final average structure required?Sincerely. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Performance of GTX 980 and 970
The 6-core Intel CPUs have only 28 PCI-E lanes rather than 40 like the 5830K/5860X which means that with a second GPU you'll get x16/x8 and with three GPUs x8/x8/x8. Also note that for the current GROMACS implementation, pairing a 5820K with two 980s will likely give a rather imbalanced hardware setup - with three 970s even more so (at least for common types of run setups). Depending on the exact use case, you may be able to make good use of 2-3 GPUs even with just a 5820K (e.g. in multi runs, one per GPU) or setups with long cut-off (or without PME), but otherwise you may not see much benefit from a second GPU, let alone a third. -- Szilárd On Mon, Sep 29, 2014 at 5:01 PM, Pappu Kumar papu...@yahoo.com wrote: Thank you for your info. I am planning to buy a computer with the following configuration: Intel 5820K Corsair H100i Hydro Cooling Performance MSI X99 SLI Plus Fractal Design R4 Seasonic X 1050W I am wondering if it would be a good idea to go for 3x GTX 970 instead of 2x GTX 980 since the cost is the same. Thank you. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] g_tune_pme_mpi is not compatible to mdrun_mpi
Hi, This all sounds super interesting. However, is there anything I can do for now or do I need to just find the best combination by hand? Thank you very much, Max -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Carsten Kutzner Sent: Montag, 29. September 2014 19:23 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] g_tune_pme_mpi is not compatible to mdrun_mpi On 29 Sep 2014, at 18:40, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, That seems suitable. Oh, it just occurred to me that on systems that use the Load Leveler, we have no means of specifying the number of MPI ranks on the command line, since 'poe' has no switch for that. So at least for this case I guess we also need to make the test optional. Carsten Mark On Mon, Sep 29, 2014 at 6:32 PM, Carsten Kutzner ckut...@gwdg.de wrote: Hi, On 29 Sep 2014, at 18:17, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, It can't be fixed, because there is no surefire way to run an arbitrary tpr on arbitrary number of ranks, regardless of how you guess -npme might succeed. What about making this check on two ranks always, regardless of what was specified on the g_tune_pme command line? On two ranks, we will never have separate PME ranks, so it should always work, since we end up with two ranks, doing PP and then PME. If the system is so small that you can not decompose it in two DD domains, there is no use to do tuning anyway. So even if you say g_tune_pme -np 48 -s input.tpr we first check with mpirun -np 2 mdrun -s input.tpr and only after that continue with -np 48. Carsten We should just make the check optional, instead of being a deal breaker. Mark On Sep 29, 2014 4:35 PM, Carsten Kutzner ckut...@gwdg.de wrote: Hi, I see where the problem is. There is an initial check in g_tune_pme to make sure that parallel runs can be executed at all. This is being run with the automatic number of PME-only ranks, which is 11 for your input file. Unfortunately, this results in 37 PP ranks, for which no domain decomposition can be found. At some point in the past we discussed that this could happen and it should be fixed. Will open a bug entry. Thanks, Carsten On 29 Sep 2014, at 15:36, Ebert Maximilian m.eb...@umontreal.ca wrote: Hi, this ist he command: setenv MDRUN mdrun_mpi g_tune_pme_mpi -np 48 -s ../eq_nvt/1ZG4_nvt.tpr -launch Here the output of perf.out P E R F O R M A N C E R E S U L T S g_tune_pme_mpi for Gromacs VERSION 5.0.1 Number of ranks : 48 The mpirun command is : mpirun Passing # of ranks via : -np The mdrun command is : mdrun_mpi mdrun args benchmarks : -resetstep 100 -o bench.trr -x bench.xtc -cpo bench.cpt -c bench.gro -e bench.edr -g bench.log Benchmark steps : 1000 dlb equilibration steps : 100 mdrun args at launchtime: Repeats for each test : 2 Input file : ../eq_nvt/1ZG4_nvt.tpr PME/PP load estimate : 0.151964 Number of particles : 39489 Coulomb type : PME Grid spacing x y z : 0.114561 0.114561 0.114561 Van der Waals type : Cut-off Will try these real/reciprocal workload settings: No. scaling rcoulomb nkx nky nkz spacing rvdw tpr file 0 1.00 1.20 72 72 72 0.12 1.20 ../eq_nvt/1ZG4_nvt_bench00.tpr 1 1.10 1.32 64 64 64 0.132000 1.32 ../eq_nvt/1ZG4_nvt_bench01.tpr 2 1.20 1.44 60 60 60 0.144000 1.44 ../eq_nvt/1ZG4_nvt_bench02.tpr Note that in addition to the Coulomb radius and the Fourier grid other input settings were also changed (see table above). Please check if the modified settings are appropriate. Individual timings for input file 0 (../eq_nvt/1ZG4_nvt_bench00.tpr): PME ranks Gcycles ns/dayPME/fRemark Cannot run the benchmark simulations! Please check the error message of mdrun for the source of the problem. Did you provide a command line argument that neither g_tune_pme nor mdrun understands? Offending command: mpirun -np 48 mdrun_mpi -npme 11 -s ../eq_nvt/1ZG4_nvt_bench00.tpr -resetstep 100 -o bench.trr -x bench.xtc -cpo bench.cpt -c bench.gro -e bench.edr -g bench.log -nsteps 1 -quiet and here are parts of the bench.log: Log file opened on Mon Sep 29 08:56:38 2014 Host: node-e1-67 pid: 24470 rank ID: 0 number of ranks: 48 GROMACS:gmx mdrun, VERSION 5.0.1 GROMACS is written by: Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar Aldert van Buuren Rudi van DrunenAnton Feenstra Sebastian Fritsch Gerrit GroenhofChristoph Junghans Peter Kasson Carsten
[gmx-users] regarding GROMACS Tutorial KALP15 in DPPC
Hello gromacs users. I am running GROMACS Tutorial of KALP15 in DPPC. I am in the step define box and solvate. after the command perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5 area_shrink1.dat i am getting an error as Use of uninitialized value $box_x in multiplication (*) at inflategro.pl line 339. Use of uninitialized value $box_y in multiplication (*) at inflategro.pl line 340. Scaling lipids There are 0 lipids... Illegal division by zero at inflategro.pl line 380. I am repeating the step third time and I am getting the same error. please help me how to skip this error. Thank you. -- *DISCLAIMER:* *This communication is intended only for the person or entity to which it is addressed and may contain confidential and / or privileged material. Any review, retransmission, dissemination or other use is prohibited. If you have received this in error, please contact the sender and delete this material from your computer. Kindly note that this mail does not constitute an offer or solicitation for the purchase or sale of any financial instrument or as an official confirmation of any transaction. The information is not warranted as to completeness or accuracy and is subject to change without notice. Any comments or statements made herein do not necessarily reflect those of Nanomedicine Research Group. Before opening the email or accessing any attachments, please check and scan for virus.* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] regarding GROMACS Tutorial KALP15 in DPPC
On 9/30/14 5:51 AM, Anurag Dobhal wrote: Hello gromacs users. I am running GROMACS Tutorial of KALP15 in DPPC. I am in the step define box and solvate. after the command perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5 area_shrink1.dat i am getting an error as Use of uninitialized value $box_x in multiplication (*) at inflategro.pl line 339. Use of uninitialized value $box_y in multiplication (*) at inflategro.pl line 340. Scaling lipids There are 0 lipids... Illegal division by zero at inflategro.pl line 380. I am repeating the step third time and I am getting the same error. please help me how to skip this error. I suggested you verify the contents of confout.gro are sensible. What did you learn? -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] g_tune_pme_mpi is not compatible to mdrun_mpi
Hi Max, On 30 Sep 2014, at 09:40, Ebert Maximilian m.eb...@umontreal.ca wrote: Hi, This all sounds super interesting. However, is there anything I can do for now or do I need to just find the best combination by hand? For now you can add the “-npme all -min 0.25 -max 0.33” options to g_tune_pme to make it work. Note that the values are just examples (further explanation in g_tune_pme -h). The idea here is that by choosing a -max value other than 0.5 (the default) you make the initial check work, then the rest will also run through. Maybe you have to play around a bit with the exact value (slightly) until you end up with something else than 37 PP ranks at the beginning. Carsten Thank you very much, Max -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Carsten Kutzner Sent: Montag, 29. September 2014 19:23 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] g_tune_pme_mpi is not compatible to mdrun_mpi On 29 Sep 2014, at 18:40, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, That seems suitable. Oh, it just occurred to me that on systems that use the Load Leveler, we have no means of specifying the number of MPI ranks on the command line, since 'poe' has no switch for that. So at least for this case I guess we also need to make the test optional. Carsten Mark On Mon, Sep 29, 2014 at 6:32 PM, Carsten Kutzner ckut...@gwdg.de wrote: Hi, On 29 Sep 2014, at 18:17, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, It can't be fixed, because there is no surefire way to run an arbitrary tpr on arbitrary number of ranks, regardless of how you guess -npme might succeed. What about making this check on two ranks always, regardless of what was specified on the g_tune_pme command line? On two ranks, we will never have separate PME ranks, so it should always work, since we end up with two ranks, doing PP and then PME. If the system is so small that you can not decompose it in two DD domains, there is no use to do tuning anyway. So even if you say g_tune_pme -np 48 -s input.tpr we first check with mpirun -np 2 mdrun -s input.tpr and only after that continue with -np 48. Carsten We should just make the check optional, instead of being a deal breaker. Mark On Sep 29, 2014 4:35 PM, Carsten Kutzner ckut...@gwdg.de wrote: Hi, I see where the problem is. There is an initial check in g_tune_pme to make sure that parallel runs can be executed at all. This is being run with the automatic number of PME-only ranks, which is 11 for your input file. Unfortunately, this results in 37 PP ranks, for which no domain decomposition can be found. At some point in the past we discussed that this could happen and it should be fixed. Will open a bug entry. Thanks, Carsten On 29 Sep 2014, at 15:36, Ebert Maximilian m.eb...@umontreal.ca wrote: Hi, this ist he command: setenv MDRUN mdrun_mpi g_tune_pme_mpi -np 48 -s ../eq_nvt/1ZG4_nvt.tpr -launch Here the output of perf.out P E R F O R M A N C E R E S U L T S g_tune_pme_mpi for Gromacs VERSION 5.0.1 Number of ranks : 48 The mpirun command is : mpirun Passing # of ranks via : -np The mdrun command is : mdrun_mpi mdrun args benchmarks : -resetstep 100 -o bench.trr -x bench.xtc -cpo bench.cpt -c bench.gro -e bench.edr -g bench.log Benchmark steps : 1000 dlb equilibration steps : 100 mdrun args at launchtime: Repeats for each test : 2 Input file : ../eq_nvt/1ZG4_nvt.tpr PME/PP load estimate : 0.151964 Number of particles : 39489 Coulomb type : PME Grid spacing x y z : 0.114561 0.114561 0.114561 Van der Waals type : Cut-off Will try these real/reciprocal workload settings: No. scaling rcoulomb nkx nky nkz spacing rvdw tpr file 0 1.00 1.20 72 72 72 0.12 1.20 ../eq_nvt/1ZG4_nvt_bench00.tpr 1 1.10 1.32 64 64 64 0.132000 1.32 ../eq_nvt/1ZG4_nvt_bench01.tpr 2 1.20 1.44 60 60 60 0.144000 1.44 ../eq_nvt/1ZG4_nvt_bench02.tpr Note that in addition to the Coulomb radius and the Fourier grid other input settings were also changed (see table above). Please check if the modified settings are appropriate. Individual timings for input file 0 (../eq_nvt/1ZG4_nvt_bench00.tpr): PME ranks Gcycles ns/dayPME/fRemark Cannot run the benchmark simulations! Please check the error message of mdrun for the source of the problem. Did you provide a command line argument that neither g_tune_pme nor mdrun understands? Offending command: mpirun -np 48 mdrun_mpi -npme 11 -s
Re: [gmx-users] regarding GROMACS Tutorial KALP15 in DPPC
Thank you Justin for your reply as per your suggestion i verified the contents in confout.gro but i was unable to check file as when i am clicking on it to open it I am getting an message that file is of unknown type. I again repeated the tutorial and I am getting the same things. Thank you again for your time. On Tue, Sep 30, 2014 at 4:16 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/30/14 5:51 AM, Anurag Dobhal wrote: Hello gromacs users. I am running GROMACS Tutorial of KALP15 in DPPC. I am in the step define box and solvate. after the command perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5 area_shrink1.dat i am getting an error as Use of uninitialized value $box_x in multiplication (*) at inflategro.pl line 339. Use of uninitialized value $box_y in multiplication (*) at inflategro.pl line 340. Scaling lipids There are 0 lipids... Illegal division by zero at inflategro.pl line 380. I am repeating the step third time and I am getting the same error. please help me how to skip this error. I suggested you verify the contents of confout.gro are sensible. What did you learn? -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- *DISCLAIMER:* *This communication is intended only for the person or entity to which it is addressed and may contain confidential and / or privileged material. Any review, retransmission, dissemination or other use is prohibited. If you have received this in error, please contact the sender and delete this material from your computer. Kindly note that this mail does not constitute an offer or solicitation for the purchase or sale of any financial instrument or as an official confirmation of any transaction. The information is not warranted as to completeness or accuracy and is subject to change without notice. Any comments or statements made herein do not necessarily reflect those of Nanomedicine Research Group. Before opening the email or accessing any attachments, please check and scan for virus.* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] regarding GROMACS Tutorial KALP15 in DPPC
On 9/30/14 7:06 AM, Anurag Dobhal wrote: Thank you Justin for your reply as per your suggestion i verified the contents in confout.gro but i was unable to check file as when i am clicking on it to open it I am getting an message that file is of unknown type. A .gro file is not simply something that you click on to magically open. It's just a listing of coordinates. Visualize it in VMD. Inspect its contents with a text editor. -Justin I again repeated the tutorial and I am getting the same things. Thank you again for your time. On Tue, Sep 30, 2014 at 4:16 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/30/14 5:51 AM, Anurag Dobhal wrote: Hello gromacs users. I am running GROMACS Tutorial of KALP15 in DPPC. I am in the step define box and solvate. after the command perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5 area_shrink1.dat i am getting an error as Use of uninitialized value $box_x in multiplication (*) at inflategro.pl line 339. Use of uninitialized value $box_y in multiplication (*) at inflategro.pl line 340. Scaling lipids There are 0 lipids... Illegal division by zero at inflategro.pl line 380. I am repeating the step third time and I am getting the same error. please help me how to skip this error. I suggested you verify the contents of confout.gro are sensible. What did you learn? -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] minimization for final configuration
Indeed, it is unlikely that averaged coordinates of certain structure versus time correspond to something physically meaningful. How do you average them, by the way? And what for, please? Dr. Vitaly V. Chaban Виталий Витальевич ЧАБАН On Tue, Sep 30, 2014 at 12:47 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/30/14 3:36 AM, Mahboobeh Eslami wrote: hi GMX users i have simulated the protein-ligand complex by gromacs for 20ns. The average for the final structure of 18 to 20 nanoseconds has been achieved.is minimization for the final average structure required?Sincerely. An average structure might be totally unphysical. Energy minimization of an unphysical structure leads you to something that is probably useless. I'd suggest doing clustering if you're interested in the predominant conformation(s) during a certain time period of the simulation. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] potassium ion in GROMOS
Dear users, How can we define potassium ion in GROMOS ions.itp file? Best, H.A -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] potassium ion in GROMOS
On 9/30/14 8:32 AM, h.aliza...@znu.ac.ir wrote: Dear users, How can we define potassium ion in GROMOS ions.itp file? Exactly like the other ions. If there are suitable K parameters, define the [moleculetype] and add the nonbonded parameters for the new atom type in ffnonbonded.itp. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Fw: minimization for final configuration
dear Justin thanks for your replyThe plot of the RMSD against time for the trajectory generated with g_rms shows a maximum RMSD about 0.195 nm. I set cut-off value to 0.2 nm for g_clusters command. Is it a appropriate value?Sincerely.On Tuesday, September 30, 2014 2:17 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/30/14 3:36 AM, Mahboobeh Eslami wrote: hi GMX users i have simulated the protein-ligand complex by gromacs for 20ns. The average for the final structure of 18 to 20 nanoseconds has been achieved.is minimization for the final average structure required?Sincerely. An average structure might be totally unphysical. Energy minimization of an unphysical structure leads you to something that is probably useless. I'd suggest doing clustering if you're interested in the predominant conformation(s) during a certain time period of the simulation. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Problems installing Gromacs 5.0.1
Hello everyone! I tried to install Gromacs 5.0.1. After this command: cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON (as described in the gromacs installation information) It tries to download of the regressiontest pack from the internet which is no longer available. I tried to turn the option off and give it the path to another set of regression tests (as cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNALOAD=OFF -DREGRESSIONTEST_PATH=/home/user/gromacs-5.0.1/build/regressiontests) but it still tries to download the file with no success. Any ideas? Thank you Cláudia Fernandes -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] regarding GROMACS Tutorial KALP15 in DPPC
Dear justin Thank you for your rely and precious time. I am aware that .gro file is to be visualized in VMD and its content can be checked in text editor. all the previous .gro file are visualized and checked in VMD. I have obetained that ( confout.gro )file by running the command of energy minimization i.e. mdrun -v -deffnm em and before this command I ran the command perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat after running the energy minimization the confout.gro is actually obetained as confout.gro.trr. so I am renaming it as confout.gro. so it is actually .trr format, which can not be visualised in VMD or checked in text editor. Please help. On Tue, Sep 30, 2014 at 4:41 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/30/14 7:06 AM, Anurag Dobhal wrote: Thank you Justin for your reply as per your suggestion i verified the contents in confout.gro but i was unable to check file as when i am clicking on it to open it I am getting an message that file is of unknown type. A .gro file is not simply something that you click on to magically open. It's just a listing of coordinates. Visualize it in VMD. Inspect its contents with a text editor. -Justin I again repeated the tutorial and I am getting the same things. Thank you again for your time. On Tue, Sep 30, 2014 at 4:16 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/30/14 5:51 AM, Anurag Dobhal wrote: Hello gromacs users. I am running GROMACS Tutorial of KALP15 in DPPC. I am in the step define box and solvate. after the command perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5 area_shrink1.dat i am getting an error as Use of uninitialized value $box_x in multiplication (*) at inflategro.pl line 339. Use of uninitialized value $box_y in multiplication (*) at inflategro.pl line 340. Scaling lipids There are 0 lipids... Illegal division by zero at inflategro.pl line 380. I am repeating the step third time and I am getting the same error. please help me how to skip this error. I suggested you verify the contents of confout.gro are sensible. What did you learn? -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- *DISCLAIMER:* *This communication is intended only for the person or entity to which it is addressed and may contain confidential and / or privileged material. Any review, retransmission, dissemination or other use is prohibited. If you have received this in error, please contact the sender and delete this material from your computer. Kindly note that this mail does not constitute an offer or solicitation for the purchase or sale of any financial instrument or as an official confirmation of any transaction. The information is not warranted as to completeness or accuracy and is subject to change without notice. Any comments or statements made herein do not necessarily reflect those of Nanomedicine Research Group. Before opening the email or accessing any attachments, please check and scan for virus.* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] regarding GROMACS Tutorial KALP15 in DPPC
On 9/30/14 10:30 AM, Anurag Dobhal wrote: Dear justin Thank you for your rely and precious time. I am aware that .gro file is to be visualized in VMD and its content can be checked in text editor. all the previous .gro file are visualized and checked in VMD. I have obetained that ( confout.gro )file by running the command of energy minimization i.e. mdrun -v -deffnm em and before this command I ran the command perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat after running the energy minimization the confout.gro is actually obetained as confout.gro.trr. so I am renaming it as confout.gro. so it is actually .trr format, which can not be visualised in VMD or checked in text editor. Which means it's an invalid input file format and that's why you're getting a failure from InflateGRO. If file names are given different extensions, you can't just randomly change them and expect things to work. If you ran mdrun -v -deffnm em you will never get anything named confout.gro. Note that the tutorial explicitly says: Then, scale down the lipids by a factor of 0.95 (assuming you have used default names, the result of the minimization is called confout.gro You didn't use default names. You told mdrun name all of my files em.* when you invoked -deffnm. If you simply ran: mdrun -s em.tpr you would get confout.gro. In any case, you should have em.gro which is what you should use to proceed. I have no idea where confout.gro.trr came from, but it's a trajectory and clearly not what needs to be used here. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Fw: minimization for final configuration
On 9/30/14 9:58 AM, Mahboobeh Eslami wrote: dear Justin thanks for your reply The plot of the RMSD against time for the trajectory generated with g_rms shows a maximum RMSD about 0.195 nm. I set cut-off value to 0.2 nm for g_clusters command. Is it a appropriate value? g_rms and g_cluster do different types of RMSD evaluation. g_rms compares against a single reference structure, g_cluster does RMSD between frames to decide on clusters, so the output of g_rms is not necessarily an indicator here. You can tell for yourself whether or not the value was suitable by inspecting the loads of output that g_cluster provides you, and by visualizing the contents of the clusters to ensure that structures that were clustered together are reasonably similar. For a structure that doesn't change much, you'll probably get one really big cluster and then a few that are sparsely populated. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Problems installing Gromacs 5.0.1
What works for me was to delete everything in the build directory before re-running cmake. Give it a try and see if that helps. --Farid 30.09.2014, 22:16, Claudia Fernandes cs.fernandes0...@gmail.com: Hello everyone! I tried to install Gromacs 5.0.1. After this command: cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON (as described in the gromacs installation information) It tries to download of the regressiontest pack from the internet which is no longer available. I tried to turn the option off and give it the path to another set of regression tests (as cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNALOAD=OFF -DREGRESSIONTEST_PATH=/home/user/gromacs-5.0.1/build/regressiontests) but it still tries to download the file with no success. Any ideas? Thank you Cláudia Fernandes -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Problems installing Gromacs 5.0.1
Hi, Spelling download with only one 'a' could help :-) Mark On Tue, Sep 30, 2014 at 4:16 PM, Claudia Fernandes cs.fernandes0...@gmail.com wrote: Hello everyone! I tried to install Gromacs 5.0.1. After this command: cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON (as described in the gromacs installation information) It tries to download of the regressiontest pack from the internet which is no longer available. I tried to turn the option off and give it the path to another set of regression tests (as cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNALOAD=OFF -DREGRESSIONTEST_PATH=/home/user/gromacs-5.0.1/build/regressiontests) but it still tries to download the file with no success. Any ideas? Thank you Cláudia Fernandes -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] watrebox with osmolites
Dear Gromacs users, Is there any tutorial to simulate a protein in water solution containing neutral zwitterionic osmolite such as trimethylglycine? Evaluating effects of the compound on protein stability/secondary structure flexibility is to be considered. Regards, Niyaz -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] watrebox with osmolites
On 9/30/14 3:31 PM, niyaz.sabir wrote: Dear Gromacs users, Is there any tutorial to simulate a protein in water solution containing neutral zwitterionic osmolite such as trimethylglycine? Evaluating effects of the compound on protein stability/secondary structure flexibility is to be considered. http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents Add your osmolyte with genbox (gmx insert-molecules in 5.0) -ci -nmol, update the topology, and solvate as usual with water. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] watrebox with osmolites
Hello, Justin, you are always so helpful, Regards, NS - Original Message - From: Justin Lemkul jalem...@vt.edu To: gmx-us...@gromacs.org; niyaz.sabir niyaz.sa...@gmail.com Sent: Wednesday, October 01, 2014 12:33 AM Subject: Re: [gmx-users] watrebox with osmolites On 9/30/14 3:31 PM, niyaz.sabir wrote: Dear Gromacs users, Is there any tutorial to simulate a protein in water solution containing neutral zwitterionic osmolite such as trimethylglycine? Evaluating effects of the compound on protein stability/secondary structure flexibility is to be considered. http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents Add your osmolyte with genbox (gmx insert-molecules in 5.0) -ci -nmol, update the topology, and solvate as usual with water. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
