Re: [gmx-users] remd- Function not implemented
On 3/11/2011 6:15 PM, 杜波 wrote: Dear teacher, when i do remd , the power is off . Then i use the commd to=21 lamboot mpirun_lam -np $to mdrun_mpi_4.5 -multi $to -replex 100 -nice 0 -cpi state.cpt -s pmma.tpr -o md -c after_md -v to continue to run the progarm. But there is a Fatal error!! Program mdrun_mpi_4.5, VERSION 4.5.5 Source code file: checkpoint.c, line: 1757 Fatal error: Failed to lock: md15.log. Function not implemented. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors lam is unsuitable for GROMACS because it does not implement the functionality required. openmpi is suggested. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] segmentation fault from power6 kernel
Thank you, Mark. Using GMX_NOOPTIMIZEDKERNELS=1 everything runs fine on power6. I also tried to run on a linux cluster and it went ok. Fabio The most likely issue is some normal blowing up scenario leading to a table-lookup-overrun segfault in the 3xx series kernels. I don't know why the usual error messages in such scenarios did not arise on this platform. Try setting the environment variable GMX_NOOPTIMIZEDKERNELS to 1 to see if this is a power6-specific kernel issue. Try running the .tpr on another platform. Mark -- Fabio Affinito, PhD SuperComputing Applications and Innovation Department CINECA - via Magnanelli, 6/3, 40033 Casalecchio di Reno (Bologna) - ITALY Tel: +39 051 6171794 Fax: +39 051 6132198 -- 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] Energy Minimisation
*Dear all, I am trying to minimize the energy of the single molecule using gromacs. I tried with the following mdp ; VARIOUS PREPROCESSING OPTIONS FOR ENERGY MINIMIZATION OF ISOLATED MOLECULE include = define = ; RUN CONTROL PARAMETERS integrator = steep nsteps = 5000 init_step= ; ENERGY MINIMIZATION OPTIONS emtol= 10 emstep = 0.01 nstcgsteep = nbfgscorr= nstcheckpoint= 100 nstlog = 100 nstenergy= 1 ; SIMULATED ANNEALING annealing = no annealing_npoints= annealing_time = annealing_temp= But it shows the following error, ERROR: The cut-off length is longer than half the shortest box vector or longer than the smallest box diagonal element. Increase the box size or decrease rlist. I have not included any the cut-off in the mdp file, but it still shows the error. Am I supposed to include something to mdp to run single molecule energy minimisation. Thank you* *With Regards, Ravi Kumar Venkatraman, IPC Dept., IISc, Bangalore, INDIA. +91-9686933963.* -- 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] source of opls Mg2+ parameters?
Hi Chris, If I remember correctly the magnesium ion parameters are the Aquvist parameters (http://pubs.acs.org/doi/abs/10.1021/j100384a009). Cheers Tom chris.ne...@utoronto.ca wrote: Dear users: does anybody know where the OPLS magnesium parameters are from? As far as I can tell, they are not in Jorgensen 1996 or Kaminski 2001, In spite of the fact that many simulation studies reference these papers for their magnesium opls parameters. In fact, I do not think that the opls mg2+ parameters in ions.itp are taken from any of the references listed in ffoplsaa.itp. I checked the following references with searches for magnesium, mg2+, and a general visual scan: ; W. L. Jorgensen, D. S. Maxwell, and J. Tirado-Rives, ; J. Am. Chem. Soc. 118, 11225-11236 (1996). ; W. L. Jorgensen and N. A. McDonald, Theochem 424, 145-155 (1998). ; W. L. Jorgensen and N. A. McDonald, J. Phys. Chem. B 102, 8049-8059 (1998). ; R. C. Rizzo and W. L. Jorgensen, J. Am. Chem. Soc. 121, 4827-4836 (1999). ; M. L. Price, D. Ostrovsky, and W. L. Jorgensen, J. Comp. Chem. (2001). ; E. K. Watkins and W. L. Jorgensen, J. Phys. Chem. A 105, 4118-4125 (2001). ; G. A. Kaminski, R.A. Friesner, J.Tirado-Rives and W.L. Jorgensen, J. Phys. Chem. B 105, 6474 (2001). From a web search, the TINKER program indicates that it uses OPLS Mg2+ parameters from an unpublished source: OPLS All-Atom Parameters for Organic Molecules, Ions, Peptides Nucleic Acids, July 2008 as provided by W. L. Jorgensen, Yale University during June 2009. These parameters are taken from those distributed with BOSS Version 4.8. (above quote from http://dasher.wustl.edu/ffe/distribution/params/oplsaa.prm ) although those tinker parameters (sigma=0.1450 and epsilon=3.9600) do not match the values for opls in the gromacs ions.itp (sigma=0.164447 and epsilon=3.66118). I did not check out BOSS directly (it costs money), but I did look at the manual on the Jorgensen web page, although that manual does not contain Mg2+ parameters. I also checked the gromos magnesium parameters that are distributed with gromacs and verified that these c6/c12 values do not match the sigma/epsilon opls values after a conversion with g_sigeps. Thank you very much for your time and assistance, Chris. -- Dr Thomas Piggot University of Southampton, UK. -- 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] Small molecule - CHARMM
Dear Gmx Users, I have produced itp file using SwissParam - for CHARMM ff. As far as I know using this topology is not a good idea and the charges of my atoms should be parametrized. My question is how to do this? Will you suggest any reading? Regards, Steven -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Simulation of membrane protein
Mark, Firstly I've downloaded Berger's dppc.itp and dppc.gro ( I've already have had gromos lipid ff) than I made pdb file for just 1 molecule of the dppc lipid consisted of 50 atoms and generate for that new molecule lipid_posres.itp via pdb2gmx than I've included lipid_posre.itp to the dppc.itp at the end of file where the reference for the posres_lipid was already existed as POSRES_LIPID. I've included in the minim.mdp define= - DPOSRES_LIPID than I've minimized my bilayer dppc.gro and checked by VMD if the bilayer was perturbed after simulation So althought posres were included in the minim.pdb the bilayer was perturbed ( tails of lipids were less ordered in comprison to the initial bilayer ) Why posres didnt work? 2011/11/2 Mark Abraham mark.abra...@anu.edu.au On 02/11/11, *James Starlight *jmsstarli...@gmail.com wrote: Justin, Mark, Ok not I've included posre only to the lipid.itp wich consist of parameters for just 1 lipid #ifdef POSRES_LIPID #include posre_lipid.itp #endif to the minim.mdp I've included define= -DPOSRES_LIPID; position restrain the lipids As the result I have not obtained any error in grompp but after minimization my lipid bilayer was perturbed. I've used very strong posres. Why it have not worked ? We can't know, because we don't know what's in any files, nor why you think the bilayer was perturbed. If you would like useful help, you need to be exhaustive in your description of what you have done, what you have observed and what you think about those. It is easier for people who might volunteer free help to do something else with their time than to ask follow-up questions when few details were given originally. Mark 2011/10/31 Justin A. Lemkul jalem...@vt.edu James Starlight wrote: I've done all of that i have posre_lipid.itp - for 1 lipid ( posres for each of 50 atoms ) I've included this in the topology of the bilayer ; Include chain topologies #include gromos53a6_lipid.ff/**forcefield.itp #include dppc.itp ; Include water topology #include gromos53a6_lipid.ff/spc.itp ; Include ion topologies #include gromos53a6_lipid.ff/ions.itp #ifdef POSRES_LIPID #include posre_lipid.itp #endif ; System specifications [ system ] 128-Lipid DMPC Bilayer in water [ molecules ] ; molecule name nr. DPPC 64 SOL 1193 SOL 690 Also I've tried to make posre for whole system ( large posres ) but it also was finished with same error Fatal error: [ file posre_lipid.itp, line 6 ]: Atom index (2) in position_restraints out of bounds (1-1). This probably means that you have inserted topology section position_restraints in a part belonging to a different molecule than you intended to. In that case move the position_restraints section to the right molecule. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/**Documentation/Errorshttp://www.gromacs.org/Documentation/Errors What's most true for such multy system. Generate posre only for 1 part or for whole system? Position restraints can only be applied on a [moleculetype] basis. Thus, order matters a lot, and the whole system cannot be restrained in one file. See the example here: http://www.gromacs.org/**Documentation/Errors#Atom_**index_n_in_position_ **restraints_out_of_boundshttp://www.gromacs.org/Documentation/Errors#Atom_index_n_in_position_restraints_out_of_bounds As it stands now, the topology you've shown tries to apply lipid position restraints after the ions have been #included, which makes no sense at all. -Justin -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- 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
Re: [gmx-users] Small molecule - CHARMM
I'm not a regular contributor, but I thought I'd comment since I just went through this exercise. I found the tutorial from the VMD group to be the easiest to follow. http://www.ks.uiuc.edu/Training/SumSchool/materials/sources/tutorials/05-qm-tutorial/part1.html This tutorial uses GAMESS, which is open source (and easy to install!). See molecularmodelingbasics.blogspot.com for detailed information to use the software, especially if you use mac. The tutorial will also teach you how to validate or correct the bond stretching force constants as well. Hope that is helpful. 2Egy On Nov 3, 2011, at 6:26 AM, Steven Neumann wrote: Dear Gmx Users, I have produced itp file using SwissParam - for CHARMM ff. As far as I know using this topology is not a good idea and the charges of my atoms should be parametrized. My question is how to do this? Will you suggest any reading? Regards, Steven -- 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] Simulation of membrane protein
1) Ensure that lipid_posres.itp was included in the topology by using grompp -pp processed.top 2) Check the content of lipid_posres.itp (often the P-atoms are restraint only and not the tails), you may post an extract of that file to the mailing list. Andreas From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of James Starlight Sent: 03 November 2011 10:33 To: Discussion list for GROMACS users Subject: Re: [gmx-users] Simulation of membrane protein Mark, Firstly I've downloaded Berger's dppc.itp and dppc.gro ( I've already have had gromos lipid ff) than I made pdb file for just 1 molecule of the dppc lipid consisted of 50 atoms and generate for that new molecule lipid_posres.itp via pdb2gmx than I've included lipid_posre.itp to the dppc.itp at the end of file where the reference for the posres_lipid was already existed as POSRES_LIPID. I've included in the minim.mdp define= - DPOSRES_LIPID than I've minimized my bilayer dppc.gro and checked by VMD if the bilayer was perturbed after simulation So althought posres were included in the minim.pdb the bilayer was perturbed ( tails of lipids were less ordered in comprison to the initial bilayer ) Why posres didnt work? 2011/11/2 Mark Abraham mark.abra...@anu.edu.au On 02/11/11, James Starlight jmsstarli...@gmail.com wrote: Justin, Mark, Ok not I've included posre only to the lipid.itp wich consist of parameters for just 1 lipid #ifdef POSRES_LIPID #include posre_lipid.itp #endif to the minim.mdp I've included define = -DPOSRES_LIPID ; position restrain the lipids As the result I have not obtained any error in grompp but after minimization my lipid bilayer was perturbed. I've used very strong posres. Why it have not worked ? We can't know, because we don't know what's in any files, nor why you think the bilayer was perturbed. If you would like useful help, you need to be exhaustive in your description of what you have done, what you have observed and what you think about those. It is easier for people who might volunteer free help to do something else with their time than to ask follow-up questions when few details were given originally. Mark 2011/10/31 Justin A. Lemkul jalem...@vt.edu James Starlight wrote: I've done all of that i have posre_lipid.itp - for 1 lipid ( posres for each of 50 atoms ) I've included this in the topology of the bilayer ; Include chain topologies #include gromos53a6_lipid.ff/forcefield.itp #include dppc.itp ; Include water topology #include gromos53a6_lipid.ff/spc.itp ; Include ion topologies #include gromos53a6_lipid.ff/ions.itp #ifdef POSRES_LIPID #include posre_lipid.itp #endif ; System specifications [ system ] 128-Lipid DMPC Bilayer in water [ molecules ] ; molecule name nr. DPPC 64 SOL 1193 SOL 690 Also I've tried to make posre for whole system ( large posres ) but it also was finished with same error Fatal error: [ file posre_lipid.itp, line 6 ]: Atom index (2) in position_restraints out of bounds (1-1). This probably means that you have inserted topology section position_restraints in a part belonging to a different molecule than you intended to. In that case move the position_restraints section to the right molecule. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors What's most true for such multy system. Generate posre only for 1 part or for whole system? Position restraints can only be applied on a [moleculetype] basis. Thus, order matters a lot, and the whole system cannot be restrained in one file. See the example here: http://www.gromacs.org/Documentation/Errors#Atom_index_n_in_position_restraints_out_of_bounds As it stands now, the topology you've shown tries to apply lipid position restraints after the ions have been #included, which makes no sense at all. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-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 list gmx-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.
Re: [gmx-users] Energy Minimisation
Ravi Kumar Venkatraman wrote: *Dear all, I am trying to minimize the energy of the single molecule using gromacs. I tried with the following mdp ; VARIOUS PREPROCESSING OPTIONS FOR ENERGY MINIMIZATION OF ISOLATED MOLECULE include = define = ; RUN CONTROL PARAMETERS integrator = steep nsteps = 5000 init_step= ; ENERGY MINIMIZATION OPTIONS emtol= 10 emstep = 0.01 nstcgsteep = nbfgscorr= nstcheckpoint= 100 nstlog = 100 nstenergy= 1 ; SIMULATED ANNEALING annealing = no annealing_npoints= annealing_time = annealing_temp= But it shows the following error, ERROR: The cut-off length is longer than half the shortest box vector or longer than the smallest box diagonal element. Increase the box size or decrease rlist. I have not included any the cut-off in the mdp file, but it still shows the error. Am I supposed to include something to mdp to run single molecule energy minimisation. You should explicitly provide the settings you wish to use. The default of 1.0 nm will be applied (which may or may not be appropriate), and the error suggests your box is too small, so you should build a proper one. http://www.gromacs.org/Documentation/Errors#The_cut-off_length_is_longer_than_half_the_shortest_box_vector_or_longer_than_the_smallest_box_diagonal_element._Increase_the_box_size_or_decrease_rlist -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] umbrella sampling restart
Hello, Can we restart the umbrella sampling simulation after some 10 or 15ns simulation using the cpt and gro files generated from the previous step. I am not sure whether it will take force generated from the previous step. Regards, Vijay. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] umbrella sampling restart
Vijayaraj wrote: Hello, Can we restart the umbrella sampling simulation after some 10 or 15ns simulation using the cpt and gro files generated from the previous step. I am not sure whether it will take force generated from the previous step. Yes, you can use a .cpt file to restart any sort of run. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Simulation of membrane protein
On 3/11/2011 9:32 PM, James Starlight wrote: Mark, Firstly I've downloaded Berger's dppc.itp and dppc.gro ( I've already have had gromos lipid ff) than I made pdb file for just 1 molecule of the dppc lipid consisted of 50 atoms and generate for that new molecule lipid_posres.itp via pdb2gmx than I've included lipid_posre.itp to the dppc.itp at the end of file where the reference for the posres_lipid was already existed as POSRES_LIPID. Your free use of lipid_posres.itp, lipid_posre.itp and posres_lipid in your sentences above make it seem like you might not have been using a file name that matches your #include. I've included in the minim.mdp define= - DPOSRES_LIPID There's an extra space in that line. There's a reason people want to see actual input and output and contents of files. Stuff filtered through your head is stuff that you might have made an extra mistake with. than I've minimized my bilayer dppc.gro and checked by VMD if the bilayer was perturbed after simulation So althought posres were included in the minim.pdb the bilayer was perturbed ( tails of lipids were less ordered in comprison to the initial bilayer ) Sounds like Andreas has the right idea. Why posres didnt work? Position restraints aren't magic - they're only applied to specific atoms. You need to choose which. The genrestr GROMACS tool may be your friend here. Mark 2011/11/2 Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au On 02/11/11, *James Starlight *jmsstarli...@gmail.com mailto:jmsstarli...@gmail.com wrote: Justin, Mark, Ok not I've included posre only to the lipid.itp wich consist of parameters for just 1 lipid #ifdef POSRES_LIPID #include posre_lipid.itp #endif to the minim.mdp I've included define= -DPOSRES_LIPID; position restrain the lipids As the result I have not obtained any error in grompp but after minimization my lipid bilayer was perturbed. I've used very strong posres. Why it have not worked ? We can't know, because we don't know what's in any files, nor why you think the bilayer was perturbed. If you would like useful help, you need to be exhaustive in your description of what you have done, what you have observed and what you think about those. It is easier for people who might volunteer free help to do something else with their time than to ask follow-up questions when few details were given originally. Mark 2011/10/31 Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu James Starlight wrote: I've done all of that i have posre_lipid.itp - for 1 lipid ( posres for each of 50 atoms ) I've included this in the topology of the bilayer ; Include chain topologies #include gromos53a6_lipid.ff/forcefield.itp #include dppc.itp ; Include water topology #include gromos53a6_lipid.ff/spc.itp ; Include ion topologies #include gromos53a6_lipid.ff/ions.itp #ifdef POSRES_LIPID #include posre_lipid.itp #endif ; System specifications [ system ] 128-Lipid DMPC Bilayer in water [ molecules ] ; molecule name nr. DPPC 64 SOL 1193 SOL 690 Also I've tried to make posre for whole system ( large posres ) but it also was finished with same error Fatal error: [ file posre_lipid.itp, line 6 ]: Atom index (2) in position_restraints out of bounds (1-1). This probably means that you have inserted topology section position_restraints in a part belonging to a different molecule than you intended to. In that case move the position_restraints section to the right molecule. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors What's most true for such multy system. Generate posre only for 1 part or for whole system? Position restraints can only be applied on a [moleculetype] basis. Thus, order matters a lot, and the whole system cannot be restrained in one file. See the example here: http://www.gromacs.org/Documentation/Errors#Atom_index_n_in_position_restraints_out_of_bounds As it stands now, the topology you've shown tries to apply lipid position restraints after the ions have been #included, which makes no sense at all. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee
Re: [gmx-users] segmentation fault from power6 kernel
On 3/11/2011 7:59 PM, Fabio Affinito wrote: Thank you, Mark. Using GMX_NOOPTIMIZEDKERNELS=1 everything runs fine on power6. I also tried to run on a linux cluster and it went ok. Sounds like a bug. Please file a report here http://redmine.gromacs.org http://redmine.gromacs.org/ including your observations and a .tpr that will reproduce them. Thanks, Mark Fabio The most likely issue is some normal blowing up scenario leading to a table-lookup-overrun segfault in the 3xx series kernels. I don't know why the usual error messages in such scenarios did not arise on this platform. Try setting the environment variable GMX_NOOPTIMIZEDKERNELS to 1 to see if this is a power6-specific kernel issue. Try running the .tpr on another platform. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] source of opls Mg2+ parameters?
Thank you Tom! Aqvist_A12 = sqrt(gromacs_C12*10^12/4.184) Aqvist_A6 = sqrt(gromacs_C6*10^6/4.184) (equation verified based on the SPC water oxygen parameters, also listed in Aqvist). This reference (Aqvist, J (1990) J. Phys. Chem., 94 (21), pp 8021?8024) should probably be noted somewhere in ions.itp or in ffoplsaa.itp. That might help stop these non-opls parameters from being cited as opls parameters. Chris. -- original message -- Hi Chris, If I remember correctly the magnesium ion parameters are the Aquvist parameters (http://pubs.acs.org/doi/abs/10.1021/j100384a009). Cheers Tom chris.ne...@utoronto.ca wrote: [Hide Quoted Text] Dear users: does anybody know where the OPLS magnesium parameters are from? As far as I can tell, they are not in Jorgensen 1996 or Kaminski 2001, In spite of the fact that many simulation studies reference these papers for their magnesium opls parameters. In fact, I do not think that the opls mg2+ parameters in ions.itp are taken from any of the references listed in ffoplsaa.itp. I checked the following references with searches for magnesium, mg2+, and a general visual scan: ; W. L. Jorgensen, D. S. Maxwell, and J. Tirado-Rives, ; J. Am. Chem. Soc. 118, 11225-11236 (1996). ; W. L. Jorgensen and N. A. McDonald, Theochem 424, 145-155 (1998). ; W. L. Jorgensen and N. A. McDonald, J. Phys. Chem. B 102, 8049-8059 (1998). ; R. C. Rizzo and W. L. Jorgensen, J. Am. Chem. Soc. 121, 4827-4836 (1999). ; M. L. Price, D. Ostrovsky, and W. L. Jorgensen, J. Comp. Chem. (2001). ; E. K. Watkins and W. L. Jorgensen, J. Phys. Chem. A 105, 4118-4125 (2001). ; G. A. Kaminski, R.A. Friesner, J.Tirado-Rives and W.L. Jorgensen, J. Phys. Chem. B 105, 6474 (2001). From a web search, the TINKER program indicates that it uses OPLS Mg2+ parameters from an unpublished source: OPLS All-Atom Parameters for Organic Molecules, Ions, Peptides Nucleic Acids, July 2008 as provided by W. L. Jorgensen, Yale University during June 2009. These parameters are taken from those distributed with BOSS Version 4.8. (above quote from http://dasher.wustl.edu/ffe/distribution/params/oplsaa.prm ) although those tinker parameters (sigma=0.1450 and epsilon=3.9600) do not match the values for opls in the gromacs ions.itp (sigma=0.164447 and epsilon=3.66118). I did not check out BOSS directly (it costs money), but I did look at the manual on the Jorgensen web page, although that manual does not contain Mg2+ parameters. I also checked the gromos magnesium parameters that are distributed with gromacs and verified that these c6/c12 values do not match the sigma/epsilon opls values after a conversion with g_sigeps. Thank you very much for your time and assistance, Chris. -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Gromacs query for vaccum medium
Let me know how to simulate a membrane protein in vaccum medium by using gromacs commands.What are the basic differences in commands as well as parameters used in liquid and vaccum medium? Please guide me. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Gromacs query for vaccum medium
On 4/11/2011 4:58 AM, Anushree Tripathi wrote: Let me know how to simulate a membrane protein in vaccum medium by using gromacs commands.What are the basic differences in commands as well as parameters used in liquid and vaccum medium? Please guide me. I suggest you do all the GROMACS tutorial material you can find, and supplement that with reading several published articles that do simulations with objectives similar to yours. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] www.gromacs.org down?
Hi gmx-users, It has been days that I cannot log into www.*gromacs*.org, does anyone know anything happed to it? Or is there any alternative website that we can see the documentation on www.*gromacs*.org/Documentation/ Thanks very much! Xiaojia -- 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] www.gromacs.org down?
mu xiaojia wrote: Hi gmx-users, It has been days that I cannot log into www.*gromacs*.org, does anyone know anything happed to it? The site has been up and down for a few days. I have contacted Rossen about it to see if he can fix it. Or is there any alternative website that we can see the documentation on www.*gromacs*.org/Documentation/ No. -Justin Thanks very much! Xiaojia -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] segmentation fault from power6 kernel
Hi Mark, today I tested the 4.5.5 version. It seems here there's not that problem. Anyway, I will take some days to make more tests. Thank you, Fabio - Messaggio originale - Da: Mark Abraham mark.abra...@anu.edu.au A: Discussion list for GROMACS users gmx-users@gromacs.org Inviato: Giovedì, 3 novembre 2011 14:40:39 Oggetto: Re: [gmx-users] segmentation fault from power6 kernel On 3/11/2011 7:59 PM, Fabio Affinito wrote: Thank you, Mark. Using GMX_NOOPTIMIZEDKERNELS=1 everything runs fine on power6. I also tried to run on a linux cluster and it went ok. Sounds like a bug. Please file a report here http://redmine.gromacs.org including your observations and a .tpr that will reproduce them. Thanks, Mark Fabio The most likely issue is some normal blowing up scenario leading to a table-lookup-overrun segfault in the 3xx series kernels. I don't know why the usual error messages in such scenarios did not arise on this platform. Try setting the environment variable GMX_NOOPTIMIZEDKERNELS to 1 to see if this is a power6-specific kernel issue. Try running the .tpr on another platform. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users 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] Steered MD in reverse direction?
Hi, I am performing steered Molecular dynamics simulation to pull a molecule out of a complex. I am using gromacs 4.5.4 to perform the constant rate pulling..I have done the steered MD simulation in a particular direction i.e hav pulled the molecule out of complex. But, to check the convergence/hysterisis of the pulled path way, I would like to perform the same steered MD in reverse direction i.e push the molecule back into the complex. But, I was wondering, to perform the backward steered MD, how should I modify the .mdp parameters? Should I make the pull_rate1 negative or switch the pull_group0 and pull_group1 ? Any help will be appreciated. The following is the part of the pull-code parameter I am using: ; Pull code pull = umbrella pull_geometry = distance ; simple distance increase pull_dim = N N Y pull_start = yes ; define initial COM distance 0 pull_ngroups = 1 pull_group0 = Mol_A pull_group1 = Mol_B pull_rate1 = 0.0025 ; 0.01 nm per ps = 10 nm per ns pull_k1 = 1000 ; kJ mol^-1 nm^-2 Sanku-- 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] Steered MD in reverse direction?
Sanku M wrote: Hi, I am performing steered Molecular dynamics simulation to pull a molecule out of a complex. I am using gromacs 4.5.4 to perform the constant rate pulling..I have done the steered MD simulation in a particular direction i.e hav pulled the molecule out of complex. But, to check the convergence/hysterisis of the pulled path way, I would like to perform the same steered MD in reverse direction i.e push the molecule back into the complex. But, I was wondering, to perform the backward steered MD, how should I modify the .mdp parameters? Should I make the pull_rate1 negative or switch the pull_group0 and pull_group1 ? Any help will be appreciated. Use a negative pull rate. But simple pulling like this can be difficult; you're now trying to hit a moving target. A slight rotation of the protein can render the whole simulation junk - your pulled molecule may smack into some undesired location. -Justin The following is the part of the pull-code parameter I am using: ; Pull code pull= umbrella pull_geometry = distance ; simple distance increase pull_dim= N N Y pull_start = yes ; define initial COM distance 0 pull_ngroups= 1 pull_group0 = Mol_A pull_group1 = Mol_B pull_rate1 = 0.0025 ; 0.01 nm per ps = 10 nm per ns pull_k1 = 1000 ; kJ mol^-1 nm^-2 Sanku -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] Steered MD in reverse direction?
Thanks for the suggestion. Also, I was wondering how one can get the time profile of the irreversible work from the gromacs pull-code out put . From constant pulling-rate SMD, we get time profile of force pullf.xvg and pullx.xvg. I wonder does multiplying the the value from pullx.xvg and value from pullf.xvg will provide the work . Or, will it be force ( obtained from pullf.xvg) multiplied by pulling rate multiplied by time ? From: Justin A. Lemkul jalem...@vt.edu To: Sanku M msank...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Thursday, November 3, 2011 9:27 PM Subject: Re: [gmx-users] Steered MD in reverse direction? Sanku M wrote: Hi, I am performing steered Molecular dynamics simulation to pull a molecule out of a complex. I am using gromacs 4.5.4 to perform the constant rate pulling..I have done the steered MD simulation in a particular direction i.e hav pulled the molecule out of complex. But, to check the convergence/hysterisis of the pulled path way, I would like to perform the same steered MD in reverse direction i.e push the molecule back into the complex. But, I was wondering, to perform the backward steered MD, how should I modify the .mdp parameters? Should I make the pull_rate1 negative or switch the pull_group0 and pull_group1 ? Any help will be appreciated. Use a negative pull rate. But simple pulling like this can be difficult; you're now trying to hit a moving target. A slight rotation of the protein can render the whole simulation junk - your pulled molecule may smack into some undesired location. -Justin The following is the part of the pull-code parameter I am using: ; Pull code pull = umbrella pull_geometry = distance ; simple distance increase pull_dim = N N Y pull_start = yes ; define initial COM distance 0 pull_ngroups = 1 pull_group0 = Mol_A pull_group1 = Mol_B pull_rate1 = 0.0025 ; 0.01 nm per ps = 10 nm per ns pull_k1 = 1000 ; kJ mol^-1 nm^-2 Sanku -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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
