[gmx-users] pbc problem
Dear jkrieger I used 2 times trjconv tool: 1) trjconv -f npt.xtc -s npt.tpr -n index.ndx -o 2npt.xtc -pbc nojump 2) trjconv -f 2npt.xtc -s npt.tpr -n index.ndx -o 3npt.xtc -pbc mol -center Dear Mark I selected all lipid atoms for centering. With my manner, pbc problem was solved just for lipids and not for drug molecule which is put inside water molecules in top leaflet. This pbc problem cause to drug molecule be in top and bottom leaflets, while I want to study translocation of the drug molecule from water to lipid bilayer. I want to solve this problem for drug molecule. If my manner is wrong, please tell me true way. 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
[gmx-users] g_hbond and g_rdf in vacuum
dear users, I am performing 500ps mdrun in vacuum for polypeptide(formed by 10-residues leucine) using gromacs_4.5.5(double-precision) using opls-aa/L force field.Input file for 500ps mdrun is given below title= peptide in vaccum cpp= /lib/cpp ; RUN CONTROL integrator = md comm_mode= ANGULAR nsteps = 50 dt= 0.001 ; NEIGHBOR SEARCHING nstlist = 0 ns_type = simple pbc = no rlist = 0 ; OUTPUT CONTROL nstxout = 1000 nstvout = 1000 nstxtcout = 0 nstlog= 1000 constraints = none nstenergy = 1000 ; OPTION FOR ELECTROSTATIC AND VDW rcoulomb = 0 ; Method for doing Van der Waals rvdw= 0 ; OPTIONS FOR WEAK COUPLING ALGORITHMS tcoupl = V-rescale tc_grps= Protein tau_t= 0.1 ref_t = 300 gen_vel= yes gen_temp = 300 Using the 500ps trajectory if i run g_hbond_d for calculating the number of hydrogen bonds as a function of time using index file(where atom O and atom N H is used) it is not working. Also if i used g_rdf_d with pbc=no using the 500ps trajectory it is also not working. I do not know why this is happening. -- santu -- 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] Output pinning for mdrun
Hi, can one output how mdrun threads are pinned to CPU cores? Thanks, Carsten -- 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] Gromos54a8
Dear all, I want to use the Gromos54A8 FF in gromacs. They are available in gromos format in http://www.gromos.net/main.pl ATB is yet to release it in gromacs format. I want to undertake the conversion of this FF to gromacs format. Apart from ConvertGromos2Gromacs.tgzhttp://www.gromacs.org/@api/deki/files/74/=ConvertGromos2Gromacs.tgzin the user contributions, I do not see any other relevant scripts. Can someone give me relevant pointers for undertaking this task? What quantities should I calculate, etc (Justin recently computed single point energies for creating a charmm36 port to gromacs...can you help me here?) Thank you. -- 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] pbc problem
On Oct 24, 2013 8:10 AM, shahab shariati shahab.shari...@gmail.com wrote: Dear jkrieger I used 2 times trjconv tool: 1) trjconv -f npt.xtc -s npt.tpr -n index.ndx -o 2npt.xtc -pbc nojump 2) trjconv -f 2npt.xtc -s npt.tpr -n index.ndx -o 3npt.xtc -pbc mol -center Dear Mark I selected all lipid atoms for centering. With my manner, pbc problem was solved just for lipids and not for drug molecule which is put inside water molecules in top leaflet. This pbc problem cause to drug molecule be in top and bottom leaflets, while I want to study translocation of the drug molecule from water to lipid bilayer. I want to solve this problem for drug molecule. There is only one water region, so upper and lower don't mean much. If you just want to see the drug and bilayer in the same PBC cell, then center on something that is central. Mark If my manner is wrong, please tell me true way. 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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_hbond and g_rdf in vacuum
Not working is too vague a symptom for anyone to guess what the problem is, sorry. Mark On Oct 24, 2013 9:39 AM, Santu Biswas santu.biswa...@gmail.com wrote: dear users, I am performing 500ps mdrun in vacuum for polypeptide(formed by 10-residues leucine) using gromacs_4.5.5(double-precision) using opls-aa/L force field.Input file for 500ps mdrun is given below title= peptide in vaccum cpp= /lib/cpp ; RUN CONTROL integrator = md comm_mode= ANGULAR nsteps = 50 dt= 0.001 ; NEIGHBOR SEARCHING nstlist = 0 ns_type = simple pbc = no rlist = 0 ; OUTPUT CONTROL nstxout = 1000 nstvout = 1000 nstxtcout = 0 nstlog= 1000 constraints = none nstenergy = 1000 ; OPTION FOR ELECTROSTATIC AND VDW rcoulomb = 0 ; Method for doing Van der Waals rvdw= 0 ; OPTIONS FOR WEAK COUPLING ALGORITHMS tcoupl = V-rescale tc_grps= Protein tau_t= 0.1 ref_t = 300 gen_vel= yes gen_temp = 300 Using the 500ps trajectory if i run g_hbond_d for calculating the number of hydrogen bonds as a function of time using index file(where atom O and atom N H is used) it is not working. Also if i used g_rdf_d with pbc=no using the 500ps trajectory it is also not working. I do not know why this is happening. -- santu -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] cant find certain atomtypes from atomtype database
On 10/24/13 1:03 AM, JuYeon wrote: dear gromacs users im using gromacs to make CS2 MD programs i made pdb file (by converting mol file to pdb file) and rtp file for CS2this is what i made pdb file COMPNDUNNAMEDAUTHORGENERATED BY OPEN BABEL 2.3.2HETATM1 C LIG 1 19.882 -4.263 -0.027 1.00 0.00 C HETATM2 S LIG 1 21.256 -5.103 -0.054 1.00 0.00 S HETATM3 S LIG 1 18.508 -3.424 0.000 1.00 0.00 S CONECT123 CONECT21 CONECT31 MASTER00000000 3030END - rtp file [ LIG ] [ atoms ]C opls_77 0 0S1 opls_202 0 0S2 opls_202 0 0 [ bonds ]C S1C S2 i attached rtp file to /usr/share/gromacs/top/oplsaa.ff/aminoacids.rtp andi added it to residuetypes.dat (which is in /usr/share/gromacs/top)then i wrote command pdb2gmx to make gro file but it failed Fatal error:Atom type opls_77 (residue LIG) not found in atomtype databaseFor more information and tips for troubleshooting, please check the GROMACSwebsite at http://www.gromacs.org/Documentation/Errors before i made rtp file, i checked atomtypes atp file which is in oplsaa.ff it says olps_77 is carbon(isobutene) and opls_202 is sulfides i dont know why gromacs cant find atom type opls_77 opls_77 does not exist. opls_077 does. The bigger problem is that you should probably not be mixing OPLS-UA parameters (opls_077) with OPLS-AA (opls_202). I suspect a better model can be built from self-consistent parameters. also, to make rtp file how to give charge and charge group to each atoms? Refer to the 2001 OPLS-AA paper for the details of the required QM calculations. The charge group is simple; the whole molecule (since it is only 3 atoms) can be one group. -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] Gromos54a8
On 10/24/13 6:43 AM, rajat desikan wrote: Dear all, I want to use the Gromos54A8 FF in gromacs. They are available in gromos format in http://www.gromos.net/main.pl ATB is yet to release it in gromacs format. I want to undertake the conversion of this FF to gromacs format. Apart from ConvertGromos2Gromacs.tgzhttp://www.gromacs.org/@api/deki/files/74/=ConvertGromos2Gromacs.tgzin the user contributions, I do not see any other relevant scripts. That's probably what you need. Is there some reason it does not work? Can someone give me relevant pointers for undertaking this task? What quantities should I calculate, etc (Justin recently computed single point energies for creating a charmm36 port to gromacs...can you help me here?) We compared potential energies (bonded and nonbonded terms individually) between the CHARMM36 force field in the latest version of the CHARMM software, then our CHARMM36 port within Gromacs. If the energies agreed, we were satisfied that the force field was implemented properly. The same would apply here - if you want to validate between the two software packages, carry out equivalent calculations in both programs. -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] Gromos54a8
Hi Justin, Thanks for the comments. Since the script was written in 2009, I don't want to use it until I verify that the formats are unchanged. The same would apply here - if you want to validate between the two software packages, carry out equivalent calculations in both programs. I didn't realize this. I do not have access to gromos software. I was thinking of reproducing the results in the 54A8 paper using gromacs. But this seems to be a critical step! Anyone in the user forum with access to gromos and interested in porting 54A8 to gromacs?? On Thu, Oct 24, 2013 at 6:01 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/24/13 6:43 AM, rajat desikan wrote: Dear all, I want to use the Gromos54A8 FF in gromacs. They are available in gromos format in http://www.gromos.net/main.pl ATB is yet to release it in gromacs format. I want to undertake the conversion of this FF to gromacs format. Apart from ConvertGromos2Gromacs.tgzhttp**://www.gromacs.org/@api/deki/**files/74/= **ConvertGromos2Gromacs.tgzhttp://www.gromacs.org/@api/deki/files/74/=ConvertGromos2Gromacs.tgz in the user contributions, I do not see any other relevant scripts. That's probably what you need. Is there some reason it does not work? Can someone give me relevant pointers for undertaking this task? What quantities should I calculate, etc (Justin recently computed single point energies for creating a charmm36 port to gromacs...can you help me here?) We compared potential energies (bonded and nonbonded terms individually) between the CHARMM36 force field in the latest version of the CHARMM software, then our CHARMM36 port within Gromacs. If the energies agreed, we were satisfied that the force field was implemented properly. The same would apply here - if you want to validate between the two software packages, carry out equivalent calculations in both programs. -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- 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] Gromos54a8
On 10/24/13 9:00 AM, rajat desikan wrote: Hi Justin, Thanks for the comments. Since the script was written in 2009, I don't want to use it until I verify that the formats are unchanged. I doubt there have been any significant changes. The same would apply here - if you want to validate between the two software packages, carry out equivalent calculations in both programs. I didn't realize this. I do not have access to gromos software. I was thinking of reproducing the results in the 54A8 paper using gromacs. But this seems to be a critical step! Reproducing published results is also a reasonable approach. Single-point energies are the most straightforward and take but a few seconds, so they are very convenient. -Justin Anyone in the user forum with access to gromos and interested in porting 54A8 to gromacs?? On Thu, Oct 24, 2013 at 6:01 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/24/13 6:43 AM, rajat desikan wrote: Dear all, I want to use the Gromos54A8 FF in gromacs. They are available in gromos format in http://www.gromos.net/main.pl ATB is yet to release it in gromacs format. I want to undertake the conversion of this FF to gromacs format. Apart from ConvertGromos2Gromacs.tgzhttp**://www.gromacs.org/@api/deki/**files/74/= **ConvertGromos2Gromacs.tgzhttp://www.gromacs.org/@api/deki/files/74/=ConvertGromos2Gromacs.tgz in the user contributions, I do not see any other relevant scripts. That's probably what you need. Is there some reason it does not work? Can someone give me relevant pointers for undertaking this task? What quantities should I calculate, etc (Justin recently computed single point energies for creating a charmm36 port to gromacs...can you help me here?) We compared potential energies (bonded and nonbonded terms individually) between the CHARMM36 force field in the latest version of the CHARMM software, then our CHARMM36 port within Gromacs. If the energies agreed, we were satisfied that the force field was implemented properly. The same would apply here - if you want to validate between the two software packages, carry out equivalent calculations in both programs. -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- == 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] Gromos54a8
Thanks Justin! If I manage to port it, I will share in the user contributions. Regards, On Thu, Oct 24, 2013 at 6:37 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/24/13 9:00 AM, rajat desikan wrote: Hi Justin, Thanks for the comments. Since the script was written in 2009, I don't want to use it until I verify that the formats are unchanged. I doubt there have been any significant changes. The same would apply here - if you want to validate between the two software packages, carry out equivalent calculations in both programs. I didn't realize this. I do not have access to gromos software. I was thinking of reproducing the results in the 54A8 paper using gromacs. But this seems to be a critical step! Reproducing published results is also a reasonable approach. Single-point energies are the most straightforward and take but a few seconds, so they are very convenient. -Justin Anyone in the user forum with access to gromos and interested in porting 54A8 to gromacs?? On Thu, Oct 24, 2013 at 6:01 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/24/13 6:43 AM, rajat desikan wrote: Dear all, I want to use the Gromos54A8 FF in gromacs. They are available in gromos format in http://www.gromos.net/main.pl ATB is yet to release it in gromacs format. I want to undertake the conversion of this FF to gromacs format. Apart from ConvertGromos2Gromacs.tgz**http**://www.gromacs.org/@api/** deki/**files/74/= http://www.gromacs.org/@api/deki/**files/74/= **ConvertGromos2Gromacs.tgzht**tp://www.gromacs.org/@api/** deki/files/74/=**ConvertGromos2Gromacs.tgzhttp://www.gromacs.org/@api/deki/files/74/=ConvertGromos2Gromacs.tgz in the user contributions, I do not see any other relevant scripts. That's probably what you need. Is there some reason it does not work? Can someone give me relevant pointers for undertaking this task? What quantities should I calculate, etc (Justin recently computed single point energies for creating a charmm36 port to gromacs...can you help me here?) We compared potential energies (bonded and nonbonded terms individually) between the CHARMM36 force field in the latest version of the CHARMM software, then our CHARMM36 port within Gromacs. If the energies agreed, we were satisfied that the force field was implemented properly. The same would apply here - if you want to validate between the two software packages, carry out equivalent calculations in both programs. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.edu jalemkul@outerbanks.** umaryland.edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/**listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchh**ttp://www.gromacs.org/Support/** Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Listshttp://www.gromacs.org/**Support/Mailing_Lists http://**www.gromacs.org/Support/**Mailing_Listshttp://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 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- 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
[gmx-users] Genion error
Hi, I have been trying to add ions to my system so as to make it neutral. However, I always obtain the same result: Solvent Group size (950) is not multiple of 9. The command I entered in this step was: genion -s protein_w.tpr -o protein_solv.gro -conc 0.15 -neutral -pname NA+ -nname CL- How could I overcome this error? I realized this problem appears to be very common; however, I could not obtain an answer for my particular issue so far. Thanks in advance for your help. Best regards, *Andrés Felipe Vásquez J., MSc.* Grupo de Fisiología Molecular Subdirección de Investigación Científica y Tecnológica Dirección de Investigación en Salud Pública Instituto Nacional de Salud Avenida calle 26 No. 51-20 - Zona 6 CAN Bogotá, D.C., Colombia -- 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] Genion error
On 10/24/13 9:34 AM, felipe vasquez wrote: Hi, I have been trying to add ions to my system so as to make it neutral. However, I always obtain the same result: Solvent Group size (950) is not multiple of 9. What group did you choose at the genion prompt? The command I entered in this step was: genion -s protein_w.tpr -o protein_solv.gro -conc 0.15 -neutral -pname NA+ -nname CL- Depending on your Gromacs version, this command may not be right. Ion names were changed as of version 4.5. -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] Genion error
Hi, I chose group 0 (System), but I also tried others like 1 (Protein) or 2 (Protein+H) with the same result. Regards, Andrés F. *Andrés Felipe Vásquez J., MSc.* Grupo de Fisiología Molecular Subdirección de Investigación Científica y Tecnológica Dirección de Investigación en Salud Pública Instituto Nacional de Salud Avenida calle 26 No. 51-20 - Zona 6 CAN Bogotá, D.C., Colombia 2013/10/24 Justin Lemkul jalem...@vt.edu On 10/24/13 9:34 AM, felipe vasquez wrote: Hi, I have been trying to add ions to my system so as to make it neutral. However, I always obtain the same result: Solvent Group size (950) is not multiple of 9. What group did you choose at the genion prompt? The command I entered in this step was: genion -s protein_w.tpr -o protein_solv.gro -conc 0.15 -neutral -pname NA+ -nname CL- Depending on your Gromacs version, this command may not be right. Ion names were changed as of version 4.5. -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Genion error
On 10/24/13 10:21 AM, felipe vasquez wrote: Hi, I chose group 0 (System), but I also tried others like 1 (Protein) or 2 (Protein+H) with the same result. You don't want to embed ions into your protein or haphazardly into the system. You'll start deleting random segments of molecules, or the command will simply fail. You need to be replacing solvent molecules (usually water). Please consult some basic tutorial material; such selections are always covered. -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] Output pinning for mdrun
Hi, No. mdrun reports the stride with which it moves over the logical cores reported by the OS, setting the affinity of GROMACS threads to logical cores, and warnings are written for various wrong-looking cases, but we haven't taken the time to write a sane report of how GROMACS logical threads and ranks are actually mapped to CPU cores. Where supported by the processor, the CPUID information is available and used in gmx_thread_affinity.c. It's just not much fun to try to report that in a way that will make sense on all possible hardware that supports CPUID - and then people will ask why it doesn't map to what their mpirun reports, get confused by hyper-threading, etc. What question were you seeking to answer? Mark On Thu, Oct 24, 2013 at 11:44 AM, Carsten Kutzner ckut...@gwdg.de wrote: Hi, can one output how mdrun threads are pinned to CPU cores? Thanks, Carsten -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Output pinning for mdrun
On Oct 24, 2013, at 4:25 PM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, No. mdrun reports the stride with which it moves over the logical cores reported by the OS, setting the affinity of GROMACS threads to logical cores, and warnings are written for various wrong-looking cases, but we haven't taken the time to write a sane report of how GROMACS logical threads and ranks are actually mapped to CPU cores. Where supported by the processor, the CPUID information is available and used in gmx_thread_affinity.c. It's just not much fun to try to report that in a way that will make sense on all possible hardware that supports CPUID - and then people will ask why it doesn't map to what their mpirun reports, get confused by hyper-threading, etc. Yes, I see. What question were you seeking to answer? Well, I just wanted to check whether my process placement is correct and that I am not getting decreased performance due to a suboptimal placement. In many cases the performance is really bad (like 50% of the expected values) if the pinning is wrong or does not work, but you never know. On some clusters there are of course tools that check and output the process placement for a dummy parallel job, or environment variables like MP_INFOLEVEL for loadleveler. Thanks! Carsten Mark On Thu, Oct 24, 2013 at 11:44 AM, Carsten Kutzner ckut...@gwdg.de wrote: Hi, can one output how mdrun threads are pinned to CPU cores? Thanks, Carsten -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users 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] pbc problem
Dear Mark Thank for your reply. If I show my system as 4 regions, my system before equilibration is as fallows: region (1): water + drug region (2): top leaflet of bilayer region (3): bottom leaflet of bilayer region (4): water After equilibration, drug molecule exits region (1) and enters region (4). Please tell me how to fix it? Which options of trjconv are appropriate for this problem? 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] pbc problem
On 10/24/13 10:57 AM, shahab shariati wrote: Dear Mark Thank for your reply. If I show my system as 4 regions, my system before equilibration is as fallows: region (1): water + drug region (2): top leaflet of bilayer region (3): bottom leaflet of bilayer region (4): water After equilibration, drug molecule exits region (1) and enters region (4). Please tell me how to fix it? Which options of trjconv are appropriate for this problem? So the drug diffused within a continuous block of solvent, is that a problem? It shouldn't be, since the system is periodic. In some cases, trjconv magic doesn't work because it shouldn't. -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] nstcalclr bug?
Hi there, I am using gromacs-4.6.1 with this mdp file: integrator = md; leap-frog integrator nsteps = 300 ; 6.0 ns dt = 0.002 ; 2 fs nstxout = 0 ; save coordinates every 10 ps nstvout = 0 ; save velocities every 10 ps nstenergy = 5000 ; save energies every 10 ps nstlog = 5000 ; update log file every 5 ps nstcalcenergy = 100 ; nstxtcout = 5000 ; xtc every 10 ps xtc_precision = 100 continuation= yes ; Restarting constraint_algorithm = lincs; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ns_type = grid ; search neighboring grid cells nstlist = 20; 10 fs rlist = 1.0 ; short-range neighborlist cutoff (in nm) rcoulomb= 1.0 ; short-range electrostatic cutoff (in nm) rvdw= 1.0 ; short-range van der Waals cutoff (in nm) nstcalclr= 10 cutoff-scheme = Group vdwtype = Cut-off vdw-modifier = Potential-shift coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT coulomb-modifier = Potential-shift tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = System; two coupling groups - more accurate tau_t = 0.1 ; time constant, in ps ref_t = 300 ; reference temperature, one for each group, in K energygrps = complex Water; group(s) to write to energy file pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT pcoupltype = isotropic ; uniform scaling of box vectors tau_p = 2.0 ; time constant, in ps ref_p = 1.0 ; reference pressure, in bar compressibility = 4.5e-5; isothermal compressibility of water, bar^-1 refcoord_scaling = com pbc = xyz ; 3-D PBC DispCorr= EnerPres ; account for cut-off vdW scheme gen_vel = no; Velocity generation is off gen-seed= 128742 ; number of steps for center of mass motion removal nstcomm = 1000 the mdout.mdp file says nstcalclr = 10, but gmxdump of the tpr file says nstcalclr = 0. If I set rvdw = 1.4 ( rlist), gmxdump of the file tpr is now correct to nstcalclr = 10. I have double checked the manual but I couldn't find the reason of this behaviour. is this a bug or am I doing wrong somewhere?? thanks for any helps and Andrea Spitaleri PhD D3 - Drug Discovery Development Istituto Italiano di Tecnologia Via Morego, 30 16163 Genova cell: +39 3485188790 -- 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] nstcalclr bug?
I think nstcalclr would only do something if you have longer range interactions to calculate (lr means longer than rlist). Therefore something has be longer than rlist for this to happen. Hi there, I am using gromacs-4.6.1 with this mdp file: integrator= md; leap-frog integrator nsteps= 300 ; 6.0 ns dt= 0.002 ; 2 fs nstxout = 0 ; save coordinates every 10 ps nstvout = 0 ; save velocities every 10 ps nstenergy = 5000 ; save energies every 10 ps nstlog= 5000 ; update log file every 5 ps nstcalcenergy = 100 ; nstxtcout = 5000 ; xtc every 10 ps xtc_precision = 100 continuation = yes ; Restarting constraint_algorithm = lincs ; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter= 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ns_type = grid ; search neighboring grid cells nstlist = 20; 10 fs rlist = 1.0 ; short-range neighborlist cutoff (in nm) rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm) rvdw = 1.0 ; short-range van der Waals cutoff (in nm) nstcalclr= 10 cutoff-scheme = Group vdwtype = Cut-off vdw-modifier = Potential-shift coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing= 0.16 ; grid spacing for FFT coulomb-modifier = Potential-shift tcoupl= V-rescale ; modified Berendsen thermostat tc-grps = System; two coupling groups - more accurate tau_t = 0.1 ; time constant, in ps ref_t = 300 ; reference temperature, one for each group, in K energygrps = complex Water; group(s) to write to energy file pcoupl= Parrinello-Rahman ; Pressure coupling on in NPT pcoupltype= isotropic ; uniform scaling of box vectors tau_p = 2.0 ; time constant, in ps ref_p = 1.0 ; reference pressure, in bar compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1 refcoord_scaling = com pbc = xyz ; 3-D PBC DispCorr = EnerPres ; account for cut-off vdW scheme gen_vel = no; Velocity generation is off gen-seed= 128742 ; number of steps for center of mass motion removal nstcomm = 1000 the mdout.mdp file says nstcalclr = 10, but gmxdump of the tpr file says nstcalclr = 0. If I set rvdw = 1.4 ( rlist), gmxdump of the file tpr is now correct to nstcalclr = 10. I have double checked the manual but I couldn't find the reason of this behaviour. is this a bug or am I doing wrong somewhere?? thanks for any helps and Andrea Spitaleri PhD D3 - Drug Discovery Development Istituto Italiano di Tecnologia Via Morego, 30 16163 Genova cell: +39 3485188790 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] meaning of the parameters in gbsa.itp
Thanks Justin for the quick hint! So, only the last two columns are needed. Sorry for the stupid question, where can I obtain reliable values for the atomic van der waals radii? Is it I have to calculate from the original force field parameters, in my case, the opls? Corina On Fri, Oct 25, 2013 at 12:04 AM, Justin Lemkul jalem...@vt.edu wrote: On 10/24/13 12:02 PM, Corina Mo wrote: Dear Gromacs users, I am interested to do implicit solvent MD but I find that some atoms (atomtype opls_961-965) in my system does not have parameters in the file gbsa.itp. Does anyone know the meaning of these columns in the file and the proper way to derive these values? ; atypesarstpi gbr hct Manual section 5.3.5 has a complete explanation and relevant literature references. -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] meaning of the parameters in gbsa.itp
Dear Gromacs users, I am interested to do implicit solvent MD but I find that some atoms (atomtype opls_961-965) in my system does not have parameters in the file gbsa.itp. Does anyone know the meaning of these columns in the file and the proper way to derive these values? ; atypesarstpi gbr hct Thanks a lot. Corina - Thanks. Corina -- View this message in context: http://gromacs.5086.x6.nabble.com/meaning-of-the-parameters-in-gbsa-itp-tp5011964.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
Re: [gmx-users] meaning of the parameters in gbsa.itp
On 10/24/13 12:02 PM, Corina Mo wrote: Dear Gromacs users, I am interested to do implicit solvent MD but I find that some atoms (atomtype opls_961-965) in my system does not have parameters in the file gbsa.itp. Does anyone know the meaning of these columns in the file and the proper way to derive these values? ; atypesarstpi gbr hct Manual section 5.3.5 has a complete explanation and relevant literature references. -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] meaning of the parameters in gbsa.itp
On 10/24/13 12:11 PM, Coco Mo wrote: Thanks Justin for the quick hint! So, only the last two columns are needed. Sorry for the stupid question, where can I obtain reliable values for the atomic van der waals radii? Is it I have to calculate from the original force field parameters, in my case, the opls? Four of the atom types you cite are carbon. Note how the radius values barely change between different carbon types. I would first start by assigning the parameters from something chemically similar. The fluorine atom is more tricky, not so much in assigning the radius, but in assigning the scaling factor. You'll have to look for advice not from the OPLS force field papers, but from the GBSA algorithm you will be using. -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] Output pinning for mdrun
On Thu, Oct 24, 2013 at 4:52 PM, Carsten Kutzner ckut...@gwdg.de wrote: On Oct 24, 2013, at 4:25 PM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, No. mdrun reports the stride with which it moves over the logical cores reported by the OS, setting the affinity of GROMACS threads to logical cores, and warnings are written for various wrong-looking cases, but we haven't taken the time to write a sane report of how GROMACS logical threads and ranks are actually mapped to CPU cores. Where supported by the processor, the CPUID information is available and used in gmx_thread_affinity.c. It's just not much fun to try to report that in a way that will make sense on all possible hardware that supports CPUID - and then people will ask why it doesn't map to what their mpirun reports, get confused by hyper-threading, etc. Yes, I see. What question were you seeking to answer? Well, I just wanted to check whether my process placement is correct and that I am not getting decreased performance due to a suboptimal placement. In many cases the performance is really bad (like 50% of the expected values) if the pinning is wrong or does not work, but you never know. GROMACS does report if its attempt to set affinities fail (and the reason), which covers some of the problem cases. Keeping MPI ranks closely associated with the hardware granularity (nodes, sockets, GPUs) will be important, but that's something to configure at the mpirun level. (Thread-MPI, being a single-node solution, has more assumptions it can make safely.) Keeping OpenMP threads within their MPI ranks pinned within hardware regions is important, but severity and solutions vary a lot with the hardware and software context (e.g. you might as well get out an abacus, as run GROMACS with OpenMP spread over a whole AMD processor, but with a single GPU then that can be the best you can do, at the moment). Key to interpreting performance results is to measure the (pinned) single-core performance, so that there is a minimum-overhead reference number for comparison. Mark On some clusters there are of course tools that check and output the process placement for a dummy parallel job, or environment variables like MP_INFOLEVEL for loadleveler. Thanks! Carsten Mark On Thu, Oct 24, 2013 at 11:44 AM, Carsten Kutzner ckut...@gwdg.de wrote: Hi, can one output how mdrun threads are pinned to CPU cores? Thanks, Carsten -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] nstcalclr bug?
Ja. No twin-range = no long-range :-) Mark On Thu, Oct 24, 2013 at 5:50 PM, jkrie...@mrc-lmb.cam.ac.uk wrote: I think nstcalclr would only do something if you have longer range interactions to calculate (lr means longer than rlist). Therefore something has be longer than rlist for this to happen. Hi there, I am using gromacs-4.6.1 with this mdp file: integrator= md; leap-frog integrator nsteps= 300 ; 6.0 ns dt= 0.002 ; 2 fs nstxout = 0 ; save coordinates every 10 ps nstvout = 0 ; save velocities every 10 ps nstenergy = 5000 ; save energies every 10 ps nstlog= 5000 ; update log file every 5 ps nstcalcenergy = 100 ; nstxtcout = 5000 ; xtc every 10 ps xtc_precision = 100 continuation = yes ; Restarting constraint_algorithm = lincs ; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter= 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ns_type = grid ; search neighboring grid cells nstlist = 20; 10 fs rlist = 1.0 ; short-range neighborlist cutoff (in nm) rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm) rvdw = 1.0 ; short-range van der Waals cutoff (in nm) nstcalclr= 10 cutoff-scheme = Group vdwtype = Cut-off vdw-modifier = Potential-shift coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing= 0.16 ; grid spacing for FFT coulomb-modifier = Potential-shift tcoupl= V-rescale ; modified Berendsen thermostat tc-grps = System; two coupling groups - more accurate tau_t = 0.1 ; time constant, in ps ref_t = 300 ; reference temperature, one for each group, in K energygrps = complex Water; group(s) to write to energy file pcoupl= Parrinello-Rahman ; Pressure coupling on in NPT pcoupltype= isotropic ; uniform scaling of box vectors tau_p = 2.0 ; time constant, in ps ref_p = 1.0 ; reference pressure, in bar compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1 refcoord_scaling = com pbc = xyz ; 3-D PBC DispCorr = EnerPres ; account for cut-off vdW scheme gen_vel = no; Velocity generation is off gen-seed= 128742 ; number of steps for center of mass motion removal nstcomm = 1000 the mdout.mdp file says nstcalclr = 10, but gmxdump of the tpr file says nstcalclr = 0. If I set rvdw = 1.4 ( rlist), gmxdump of the file tpr is now correct to nstcalclr = 10. I have double checked the manual but I couldn't find the reason of this behaviour. is this a bug or am I doing wrong somewhere?? thanks for any helps and Andrea Spitaleri PhD D3 - Drug Discovery Development Istituto Italiano di Tecnologia Via Morego, 30 16163 Genova cell: +39 3485188790 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users 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: meaning of the parameters in gbsa.itp
Dear Justin, Thanks again! Will look into it. Btw, you know if there is any plan to implement implicit lipid model in GROMACS? Corina On Fri, Oct 25, 2013 at 12:17 AM, Justin Lemkul [via GROMACS] ml-node+s5086n5011968...@n6.nabble.com wrote: On 10/24/13 12:11 PM, Coco Mo wrote: Thanks Justin for the quick hint! So, only the last two columns are needed. Sorry for the stupid question, where can I obtain reliable values for the atomic van der waals radii? Is it I have to calculate from the original force field parameters, in my case, the opls? Four of the atom types you cite are carbon. Note how the radius values barely change between different carbon types. I would first start by assigning the parameters from something chemically similar. The fluorine atom is more tricky, not so much in assigning the radius, but in assigning the scaling factor. You'll have to look for advice not from the OPLS force field papers, but from the GBSA algorithm you will be using. -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=5011968i=0 | (410) 706-7441 == -- gmx-users mailing list[hidden email]http://user/SendEmail.jtp?type=nodenode=5011968i=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=5011968i=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/meaning-of-the-parameters-in-gbsa-itp-tp5011964p5011968.html To unsubscribe from meaning of the parameters in gbsa.itp, click herehttp://gromacs.5086.x6.nabble.com/template/NamlServlet.jtp?macro=unsubscribe_by_codenode=5011964code=Y29jb21vc2FuQGdtYWlsLmNvbXw1MDExOTY0fDYxMjc2MzE0MQ== . 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 - Thanks. Corina -- View this message in context: http://gromacs.5086.x6.nabble.com/meaning-of-the-parameters-in-gbsa-itp-tp5011964p5011969.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
Re: [gmx-users] pbc problem
As Justin said, there is no actual division between region 1 and 4. Apparently you got the free diffusion you asked for! :-) Mark On Thu, Oct 24, 2013 at 4:57 PM, shahab shariati shahab.shari...@gmail.comwrote: Dear Mark Thank for your reply. If I show my system as 4 regions, my system before equilibration is as fallows: region (1): water + drug region (2): top leaflet of bilayer region (3): bottom leaflet of bilayer region (4): water After equilibration, drug molecule exits region (1) and enters region (4). Please tell me how to fix it? Which options of trjconv are appropriate for this problem? 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 -- 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] Output pinning for mdrun
Hi Carsten, On Thu, Oct 24, 2013 at 4:52 PM, Carsten Kutzner ckut...@gwdg.de wrote: On Oct 24, 2013, at 4:25 PM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, No. mdrun reports the stride with which it moves over the logical cores reported by the OS, setting the affinity of GROMACS threads to logical cores, and warnings are written for various wrong-looking cases, but we haven't taken the time to write a sane report of how GROMACS logical threads and ranks are actually mapped to CPU cores. Where supported by the processor, the CPUID information is available and used in gmx_thread_affinity.c. It's just not much fun to try to report that in a way that will make sense on all possible hardware that supports CPUID - and then people will ask why it doesn't map to what their mpirun reports, get confused by hyper-threading, etc. Yes, I see. What question were you seeking to answer? Well, I just wanted to check whether my process placement is correct and that I am not getting decreased performance due to a suboptimal placement. In many cases the performance is really bad (like 50% of the expected values) if the pinning is wrong or does not work, but you never know. That could very well be the result of two software threads pinned to that same hardware thread. You can use hwloc-ps to display the mapping of thread and process ID-s to hardware entities (core, socket, NUMA domain, etc.). However, this will still not give you the full picture, that is the mdrun thread ID - OS thread ID - hardware thread/core mapping, as you can't know which OS thread corresponds to which software thread. I have some code in a pending (and for now blocked) change: https://gerrit.gromacs.org/#/c/2633/ in src/gmxlib/gmx_thread_affinity.c:print_current_proc_thread_binding(). Let me know if that worked. Cheers, -- Szilárd On some clusters there are of course tools that check and output the process placement for a dummy parallel job, or environment variables like MP_INFOLEVEL for loadleveler. Thanks! Carsten Mark On Thu, Oct 24, 2013 at 11:44 AM, Carsten Kutzner ckut...@gwdg.de wrote: Hi, can one output how mdrun threads are pinned to CPU cores? Thanks, Carsten -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: a new GROMACS simulation tool
Hi I would like to try it out Srinivasa Rao Penumutchu Research Scholar Protein NMR Lab , II floor-218 Department of Chemistry National Tsing Hua University, Hsinchu, Taiwan. Ph: 886357151-35605, Email- penumutchu.srini...@gmail.com ,s9923...@m99.nthu.edu.tw -- View this message in context: http://gromacs.5086.x6.nabble.com/a-new-GROMACS-simulation-tool-tp5011910p5011974.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] 2D umbrella sampling simulation
Your restraint involving group C should use pull_group2, etc, not another copy of pull_group1. Other than that, it looks like a valid approach. Chris. -- original message -- I am going to perform the two-dimensional umbrella sampling using a pair of distances (the distance btw atoms A and B, C and B) in the restraints. Could someone please tell whether I can use the current pull code as follows? - ; Pull code pull= umbrella pull_geometry = distance pull_dim= Y Y Y pull_start = no pull_ngroups= 2 pull_group0 = B pull_group1 = A ;restraint of distance btw A and B pull_init1 = 2.7 ;equilibrium distance of A-B pull_rate1 = 0.0 pull_k1 = 2000 ; kJ mol^-1 nm^-2 pull_group1 = C ;restraint of distance btw C and B pull_init1 = 3.7 ;equilibrium distance of C-B pull_rate1 = 0.0 pull_k1 = 2500 ; kJ mol^-1 nm^-2 pull_nstxout= 1000 ; every 2 ps pull_nstfout= 1000 ; every 2 ps - Many thanks. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
