Re: [gmx-users] Error in Ligand position restraints
Hello All I am trying to perform MD for protein ligand protein complex in popc lipid with charmm36 force field and also follow Justin A. Lemkul tutorial. I successfully performed till perl inflategro.pl system.gro 4 POPC 0 system_inflated.gro 5 area.dat After this when I started performing energy minimization part it gives error : Fatal error: [ file strong_posre.itp, line 6979 ]: Atom index (6975) in position_restraints out of bounds (1-6974). 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. I think the problem is that I have included position restraints for protein in topology file but not includes position restraints for ligand in that file. when I added ; Strong position restraints for InflateGRO #ifdef STRONG_POSRES #include strong_posre.itp #endif to my topology file it consider both protein and ligand so the number of residue present in my position restraint file and Strong position restraint is different. I also check it by adding position restraint for ligand in my topology file. but it still giving the same error. I also check by merging position restraint file for ligand and protein but the same error is present. This is my topology file: ; Include forcefield parameters #include charmm36_lipid.ff/forcefield.itp ; Include ligand topology #include lig.itp [ moleculetype ] ; Namenrexcl Protein 3 [ atoms ] ... ... ... ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ; Ligand position restraints #ifdef POSRES #include posre_lig.itp #endif ; Strong position restraints for InflateGRO #ifdef STRONG_POSRES #include strong_posre.itp #endif ; Include POPC chain topology #include popc.itp ; Include water topology #include charmm36_lipid.ff/tip3p.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include charmm36_lipid.ff/ions.itp [ system ] ; Name Gyas ROwers Mature At Cryogenic Speed [ molecules ] ; Compound#mols Protein 1 lig 1 POPC128 I have also check by changing the position of lig.itp file and posre_lig file by keeping them together like ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ; Include ligand topology #include lig.itp ; Ligand position restraints #ifdef POSRES #include posre_lig.itp #endif then it gives another error because of the change in position of ligand topology file. Fatal error: Syntax error - File cyc.itp, line 7 Last line read: '[ atomtypes ] ' Invalid order for directive atomtypes Please Help. Thanks in Advance With Regards Neha bharty -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] atoms are not part of any of the T-Coupling groups
Hello all, I am working on protein with two chains. I would like to restrain one atom of one chain while doing steered MD. For the same reason, I have created an index file that includes that atom, then created its posre.itp file and finally included following lines at the end of topol_Protein_chainA.itp: ; Include Position restraint file #ifdef POSRES_CA_chA_r131 #include posre.itp #endif I am also pasting a small section of my topol.top file: ; Include forcefield parameters #include gromos53a6.ff/forcefield.itp ; Include chain topologies #include topol_Protein_chain_A.itp #include topol_Protein_chain_B.itp #include topol_Ion_chain_A2.itp #include topol_Ion_chain_B2.itp ; Include water topology #include gromos53a6.ff/spc.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif After carrying out NPT equilibration, when I run following command: grompp -f md_pull.mdp -c npt.gro -p topol.top -n index.ndx -t npt.cpt -o pull.tpr as given in tutorial: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/05_pull.html I am getting following error: 215400 atoms are not part of any of the T-Coupling groups Since my pull.mdp file as the same as given in tutorial, my coupling groups are Protein and Non-Protein. I suspect there is something wrong while adding restraints using include file mechanism. Please help me resolve the problem. Thanks Nidhi -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Suggestions for Gromacs Perfomance
Dear gmx users, I have been performing some benchmarks as given taken from following URL, http://www.gromacs.org/GPU_acceleration The expected performance values is taken from the graph s . This cluster has a two nodes, of which one has two Nvidia K20 gpus. I have follo wed the performance checklist given in following URL, http://www. gromacs.org/Documentation/Performance_checklist http://www.gromacs.org/Documentation/Performance_checklist I am using fftw-3.3.4 with sse2 SIMD instructions and using cuda-5.5. The results are as follows: Gromacs Version 4.6.5 GCC Version 4.4.6 System CPU/GPU used performance(ns/day) expected(ns/day) RNASE 2 CPU (Cores 16, nopm 1) 63.815 80 RNASE 1CPU(8cores)+1GPU (-gpu_id ) 50.647 95 ADH 4 CPU on 2 on each node (32 Cores) 15.115 15 Gromacs Version 5.0.0 GCC Version 4.7.2 System CPU/GPU used performance(ns/day) expected(ns/day) RNASE 2 CPU (Cores 16, nopm 1)66.698 80 RNASE 1CPU(8cores)+1GPU (-np 8 -gpu_id ) 47.763 95 ADH 4 CPU on 2 on each node (32 Cores) 14.142 15 Kindly provide inputs to improve the performance with gpus . Also, if possible please suggest simulation with reported performance simulation for performing benchmarks for both CPU GPU. Regards, Dinesh Mali -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Error in system_inflate.gro coordinates does not match
hello every one i am working on complex with popc membrane i got error in Deuterium Order Parameters group 1 does not have same number of elements as grp 1 i used the command make_ndx -f md_0_1.tpr -o sn1.ndx 0 System : 38483 atoms 1 Protein : 3873 atoms 2 Protein-H : 3061 atoms 3 C-alpha : 408 atoms 4 Backbone: 1224 atoms 5 MainChain : 1633 atoms 6 MainChain+Cb: 2015 atoms 7 MainChain+H : 2000 atoms 8 SideChain : 1873 atoms 9 SideChain-H : 1428 atoms 10 Prot-Masses : 3873 atoms 11 non-Protein : 34610 atoms 12 Other : 6365 atoms 13 UNK :21 atoms 14 POPC: 6344 atoms 15 CL :15 atoms 16 Water : 28230 atoms 17 SOL : 28230 atoms 18 non-Water : 10253 atoms 19 Ion :15 atoms 20 UNK :21 atoms 21 POPC: 6344 atoms 22 CL :15 atoms 23 Water_and_ions : 28245 atoms nr : group ! 'name' nr name 'splitch' nrEnter: list groups 'a': atom 'del' nr 'splitres' nr 'l': list residues 't': atom type | 'keep' nr'splitat' nr'h': help 'r': residue 'res' nr 'chain' char name: group'case': case sensitive 'q': save and quit 'ri': residue index aC34 Found 122 atoms with name C34 24 C34 : 122 atoms aC36 Found 122 atoms with name C36 25 C36 : 122 atoms a C37 Found 122 atoms with name C37 26 C37 : 122 atoms a C38 Found 122 atoms with name C38 27 C38 : 122 atoms a C39 Found 122 atoms with name C39 28 C39 : 122 atoms a C40 Found 122 atoms with name C40 29 C40 : 122 atoms a C41 Found 122 atoms with name C41 30 C41 : 122 atoms a C42 Found 122 atoms with name C42 31 C42 : 122 atoms A C43 Syntax error: A C43 a C43 Found 122 atoms with name C43 32 C43 : 122 atoms a C44 Found 122 atoms with name C44 33 C44 : 122 atoms a C45 Found 122 atoms with name C45 34 C45 : 122 atoms a C46 Found 122 atoms with name C46 35 C46 : 122 atoms a C47 Found 122 atoms with name C47 36 C47 : 122 atoms a C48 Found 122 atoms with name C48 37 C48 : 122 atoms a C49 Found 122 atoms with name C49 38 C49 : 122 atoms a C50 Found 122 atoms with name C50 39 C50 : 122 atoms a CA1 Found 122 atoms with name CA1 40 CA1 : 122 atoms a CA2 Found 122 atoms with name CA2 41 CA2 : 122 atoms del 0-21 Removed group 0 'System' Removed group 1 'Protein' Removed group 2 'Protein-H' Removed group 3 'C-alpha' Removed group 4 'Backbone' Removed group 5 'MainChain' Removed group 6 'MainChain+Cb' Removed group 7 'MainChain+H' Removed group 8 'SideChain' Removed group 9 'SideChain-H' Removed group 10 'Prot-Masses' Removed group 11 'non-Protein' Removed group 12 'Other' Removed group 13 'UNK' Removed group 14 'POPC' Removed group 15 'CL' Removed group 16 'Water' Removed group 17 'SOL' Removed group 18 'non-Water' Removed group 19 'Ion' Removed group 20 'UNK' Removed group 21 'POPC' q 0 System : 38483 atoms 1 Protein : 3873 atoms 2 Protein-H : 3061 atoms 3 C-alpha : 408 atoms 4 Backbone: 1224 atoms 5 MainChain : 1633 atoms 6 MainChain+Cb: 2015 atoms 7 MainChain+H : 2000 atoms 8 SideChain : 1873 atoms 9 SideChain-H : 1428 atoms 10 Prot-Masses : 3873 atoms 11 non-Protein : 34610 atoms 12 Other : 6365 atoms 13 UNK :21 atoms 14 POPC: 6344 atoms 15 CL :15 atoms 16 Water : 28230 atoms 17 SOL : 28230 atoms 18 non-Water : 10253 atoms 19 Ion :15 atoms 20 UNK :21 atoms 21 POPC: 6344 atoms 22 CL :15 atoms 23 Water_and_ions : 28245 atoms nr : group ! 'name' nr name 'splitch' nrEnter: list groups 'a': atom 'del' nr 'splitres' nr 'l': list residues 't': atom type | 'keep' nr'splitat' nr'h': help 'r': residue 'res' nr 'chain' char name: group'case': case sensitive 'q': save and quit 'ri': residue index a C15 Found 122 atoms with name C15 24 C15 : 122 atoms a C17 Found 122 atoms with name C17 25 C17 : 122 atoms a C18 Found 122 atoms with name C18 26 C18 :
[gmx-users] Pressures after NPT
dear gromacs users, I did an NPT equilibration of 100ps with a reference pressure of 1bar. After the equilibration, my average pressure was 1.2 bar. But when I started my production run (with a reference pressure of 1 bar) my pressure was rising (and falling) again. for the first 50 ps, the average pressure was -7.2 bar. Then after a 100ps of production run the pressure was -0.84 bar. I have two questions regrading this- 1. Does negative pressure mean anything wrong with my system? or should I just take the magnitude of my pressure? 2. After the NPT my average pressure was rising again(but eventually came close to its reference value after some time), should it happen in a stable simulation? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Simulation of Glass Surfaces?
On 8/6/14, 8:01 AM, AJ Lanphere wrote: Thank you for the information that does sound like it would do what I'm looking for, but could you possibly elaborate on how to set that up? I don't see either of those terms in the manual, either under the run parameters section about walls or otherwise. Manual section 4.3.2 and Table 5.5. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Protein simulation including ligand with Fe(III)
Hello again, Since I could not find any reliable parameters for the Fe-O for the GROMOS 96 forcefield I decided to modify it to use the parameters for its Fe-N in its HEME group. While reading through the gromos54a7 files i saw that it has parameters for the Fe-O bond so I thought that it might be able to deal with my molecule. I run pdb2gmx on my molecule, which included the protein and the iron, and a topology was produced, giving no errors. However, when I opened the topology, there is no Fe present in it. Sorry if that's a silly question but shouldn't it be in there? I can include the files if required. Thanks again. Nicholas -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Pressures after NPT
On 8/6/14, 4:54 AM, ibrahim khalil wrote: dear gromacs users, I did an NPT equilibration of 100ps with a reference pressure of 1bar. After the equilibration, my average pressure was 1.2 bar. But when I started my production run (with a reference pressure of 1 bar) my pressure was rising (and falling) again. for the first 50 ps, the average pressure was -7.2 bar. Then after a 100ps of production run the pressure was -0.84 bar. I have two questions regrading this- 1. Does negative pressure mean anything wrong with my system? or should I just take the magnitude of my pressure? Positive and negative correspond to expansion and contraction. 2. After the NPT my average pressure was rising again(but eventually came close to its reference value after some time), should it happen in a stable simulation? Pressure fluctuates wildly in a simulation. See http://www.gromacs.org/Documentation/Terminology/Pressure. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Simulation of Glass Surfaces?
I suppose I should have mentioned I'm using Gromacs 4.6.5. That section of the manual covers angular restraints, is that where I should be reading? Sorry for asking potentially inane questions, I'm not very experienced with this sort of thing. On Wed, Aug 6, 2014 at 10:18 AM, Justin Lemkul jalem...@vt.edu wrote: On 8/6/14, 8:01 AM, AJ Lanphere wrote: Thank you for the information that does sound like it would do what I'm looking for, but could you possibly elaborate on how to set that up? I don't see either of those terms in the manual, either under the run parameters section about walls or otherwise. Manual section 4.3.2 and Table 5.5. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Simulation of Glass Surfaces?
On 8/6/14, 8:28 AM, AJ Lanphere wrote: I suppose I should have mentioned I'm using Gromacs 4.6.5. That section of the manual covers angular restraints, is that where I should be reading? Sorry for asking potentially inane questions, I'm not very experienced with this sort of thing. You need 5.0 for flat-bottom potentials. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Error in Ligand position restraints
On 8/6/14, 3:03 AM, neha bharti wrote: Hello All I am trying to perform MD for protein ligand protein complex in popc lipid with charmm36 force field and also follow Justin A. Lemkul tutorial. I successfully performed till perl inflategro.pl system.gro 4 POPC 0 system_inflated.gro 5 area.dat After this when I started performing energy minimization part it gives error : Fatal error: [ file strong_posre.itp, line 6979 ]: Atom index (6975) in position_restraints out of bounds (1-6974). 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. I think the problem is that I have included position restraints for protein in topology file but not includes position restraints for ligand in that file. when I added ; Strong position restraints for InflateGRO #ifdef STRONG_POSRES #include strong_posre.itp #endif to my topology file it consider both protein and ligand so the number of residue present in my position restraint file and Strong position restraint is different. I also check it by adding position restraint for ligand in my topology file. but it still giving the same error. I also check by merging position restraint file for ligand and protein but the same error is present. This is my topology file: ; Include forcefield parameters #include charmm36_lipid.ff/forcefield.itp ; Include ligand topology #include lig.itp [ moleculetype ] ; Namenrexcl Protein 3 [ atoms ] ... ... ... ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ; Ligand position restraints #ifdef POSRES #include posre_lig.itp #endif The topology is organized incorrectly. A [position_restraints] directive must be declared immediately after the [moleculetype] to which it belongs, using the atom numbering of the [moleculetype], NOT the global numbering. http://www.gromacs.org/Documentation/Errors#Atom_index_n_in_position_restraints_out_of_bounds ; Strong position restraints for InflateGRO #ifdef STRONG_POSRES #include strong_posre.itp #endif ; Include POPC chain topology #include popc.itp ; Include water topology #include charmm36_lipid.ff/tip3p.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include charmm36_lipid.ff/ions.itp [ system ] ; Name Gyas ROwers Mature At Cryogenic Speed [ molecules ] ; Compound#mols Protein 1 lig 1 POPC128 I have also check by changing the position of lig.itp file and posre_lig file by keeping them together like ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ; Include ligand topology #include lig.itp ; Ligand position restraints #ifdef POSRES #include posre_lig.itp #endif then it gives another error because of the change in position of ligand topology file. Fatal error: Syntax error - File cyc.itp, line 7 Last line read: '[ atomtypes ]' Invalid order for directive atomtypes The ligand topology must be declared immediately after the #include statement for the force field if it introduces new atom types. Thus, the position restraint file must be moved up accordingly. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] atoms are not part of any of the T-Coupling groups
On 8/6/14, 3:46 AM, Nidhi Katyal wrote: Hello all, I am working on protein with two chains. I would like to restrain one atom of one chain while doing steered MD. For the same reason, I have created an index file that includes that atom, then created its posre.itp file and finally included following lines at the end of topol_Protein_chainA.itp: ; Include Position restraint file #ifdef POSRES_CA_chA_r131 #include posre.itp #endif I am also pasting a small section of my topol.top file: ; Include forcefield parameters #include gromos53a6.ff/forcefield.itp ; Include chain topologies #include topol_Protein_chain_A.itp #include topol_Protein_chain_B.itp #include topol_Ion_chain_A2.itp #include topol_Ion_chain_B2.itp ; Include water topology #include gromos53a6.ff/spc.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif After carrying out NPT equilibration, when I run following command: grompp -f md_pull.mdp -c npt.gro -p topol.top -n index.ndx -t npt.cpt -o pull.tpr as given in tutorial: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/05_pull.html I am getting following error: 215400 atoms are not part of any of the T-Coupling groups Since my pull.mdp file as the same as given in tutorial, my coupling groups are Protein and Non-Protein. I suspect there is something wrong while adding restraints using include file mechanism. Please help me resolve the problem. The error is not a result of the #include mechanism; it's a problem in the group definitions, either in the .mdp file or in the index file. Without the full text of the .mdp and the gmxcheck output of the index.ndx file, there's little to suggest. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Protein simulation including ligand with Fe(III)
On 8/6/14, 8:19 AM, Nikolaos Michelarakis wrote: Hello again, Since I could not find any reliable parameters for the Fe-O for the GROMOS 96 forcefield I decided to modify it to use the parameters for its Fe-N in its HEME group. While reading through the gromos54a7 files i saw that it has parameters for the Fe-O bond so I thought that it might be able to deal with my molecule. I run pdb2gmx on my molecule, which included the protein and the iron, and a topology was produced, giving no errors. However, when I opened the topology, there is no Fe present in it. Sorry if that's a silly question but shouldn't it be in there? I can include the files if required. Indeed, that makes no sense at all. Please post the topology and input coordinate files for download on a file-sharing service. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Simulation of Glass Surfaces?
Alright, so that might not be an option for me. Can I configure the walls to accomplish a similar result in 4.6.5? On Wed, Aug 6, 2014 at 10:30 AM, Justin Lemkul jalem...@vt.edu wrote: On 8/6/14, 8:28 AM, AJ Lanphere wrote: I suppose I should have mentioned I'm using Gromacs 4.6.5. That section of the manual covers angular restraints, is that where I should be reading? Sorry for asking potentially inane questions, I'm not very experienced with this sort of thing. You need 5.0 for flat-bottom potentials. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] User-PME
Hi, Haven't looked at the code, but the table maps to the real space part only, because it shares the implementation with the other kinds of user tables, for which reciprocal-space considerations do not apply. Mark On Wed, Aug 6, 2014 at 8:36 AM, O'Neill, David d.o-ne...@warwick.ac.uk wrote: Hello gromacs users, I have a question about the mdp option User-PME. I am right in saying that if I choose a potential for the electrostatics, f(r) in my user tables, it is just for the real space part of the Ewald sum and then User-PME calculates the reciprocal and self-correction terms? Or do I need to include these in the f(r) function in my user tables? Any help is much appreciated. Regards David -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Why is there a NxN VdW [F] on a separate line?
On Tue, Aug 5, 2014 at 9:24 PM, Theodore Si sjyz...@gmail.com wrote: Please compare the file 8.log https://onedrive.live.com/ redir?resid=990FCE59E48164A4%212481authkey=%21AI9ThbRY_ 7ZgAg8ithint=file%2clog and 512.log https://onedrive.live.com/ redir?resid=990FCE59E48164A4%212482authkey=% 21APLkizOBzXtPHxsithint=file%2clog. These runs report the use of 8 MPI ranks with 2 OpenMP threads per rank, and 512 MPI ranks with 1 OpenMP thread per rank. GROMACS (like a lot of codes) use hybrid MPI/OpenMP parallelism, and when describing a run it is normally incorrect to mention only one aspect. Their M E G A - F L O P S A C C O U N T I N part are different as 8.log has no standalone NxN VdW [F] and NxN VdW [VF]. 512.log has the following lines. NxN VdW [F] 17.077648 563.562 0.0 NxN VdW [VF]0.002592 0.111 0.0 Why the difference? They report on calls to different kernels. Only the forces are required for MD. Energies (ie. V) are extra work, so they're only done when necessary. This was a key optimization in 4.6. In your run, they were not often required. And the both have NxN Ewald Elec. + VdW [F] NxN Ewald Elec. + VdW [VF] Does NxN Ewald Elec. + VdW [F] mean NxN Ewald Elec. and NxN VdW [F]? If it is the case, why 512.log has both NxN Ewald Elec. + VdW [F] and NxN VdW [F]? They report on the calls to different kernels. If you have a chunk of atoms that don't have charges, you'd be pretty happy to call a kernel that didn't waste time doing that. Likewise if you don't need the energy, mdrun doesn't compute it. This is discovered at run time, so if you distribute the work to different numbers of compute units, then one of them might end up with some clusters that only have atoms that lack charge. The clustering is opportunistic, so differences are expected. In your next runs, you might observe the opposite behaviour. That said, the flops output is scarcely meaningful (even if the reporting is accurate). Performance is dominated by considerations of load balance, and the subsequent information deals with that. Mark On 8/5/2014 10:11 PM, Mark Abraham wrote: On Tue, Aug 5, 2014 at 4:00 AM, Theodore Si sjyz...@gmail.com wrote: This is extracted from a log file There's no data. The list cannot accept attachments, so you need to copy-paste a relevant chunk, or upload a log file to a file-sharing service. of a mdrun of 512 openMP threads without GPU acceleration. mdrun will refuse to run with 512 OpenMP threads - please report your mdrun command line rather than your mental model of it. Since the first line and third line both have N*N Vdw [F], does the former include the latter? No, but there is no line with N*N Vdw [F]. Please be precise if you are asking for detailed information. As we can see, in the log file of a mdrun of 8 openMP threads without GPU acceleration, there is no standalone N*N Vdw [F], why the difference? Can't tell, don't know what is different between the two runs. My guess is that the former run is actually running on 64 MPI ranks, each of 8 OpenMP threads, in which case you have domain decomposition per MPI rank, and in that case there are separate calls to kernels that are aimed at computing the interactions associated with atoms whose home is in different domains. You should see the ratio vary as the number of ranks varies. Mark -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Protein simulation including ligand with Fe(III)
On 8/6/14, 9:26 AM, Nikolaos Michelarakis wrote: Here are the links: https://drive.google.com/file/d/0BzqRbRx4Ynf0c28zYVhoY3JRenM/edit?usp=sharing for the pdb file. The line for FE is misformatted (all the columns are aligned incorrectly), so it is simply ignored. -Justin https://drive.google.com/file/d/0BzqRbRx4Ynf0TmNsckliYWtqQUU/edit?usp=sharing for the topology. Cheers! -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] User-PME
Mark, Thankyou for your response. Knowing this makes my life much easier, although I will of course run a test system to check. Regards, David From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Mark Abraham mark.j.abra...@gmail.com Sent: 06 August 2014 16:10 To: Discussion list for GROMACS users Subject: Re: [gmx-users] User-PME Hi, Haven't looked at the code, but the table maps to the real space part only, because it shares the implementation with the other kinds of user tables, for which reciprocal-space considerations do not apply. Mark On Wed, Aug 6, 2014 at 8:36 AM, O'Neill, David d.o-ne...@warwick.ac.uk wrote: Hello gromacs users, I have a question about the mdp option User-PME. I am right in saying that if I choose a potential for the electrostatics, f(r) in my user tables, it is just for the real space part of the Ewald sum and then User-PME calculates the reciprocal and self-correction terms? Or do I need to include these in the f(r) function in my user tables? Any help is much appreciated. Regards David -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] New residue in FF does not bond to others.
Cause now what happens is that grompp requires bonding parameters for atoms which are actually bonded and for which are not (angle and dihedral parameters), e.g. CH6-Ser69 and CH6-Phe65 is what I want but I do not want connection between Ser69-Phe65. Now grompp asks me about bonding paramters for atoms which build all three residues while these residues are separated by more than 4 atoms. Best wishes, Dawid 2014-08-06 18:49 GMT+01:00 Dawid das add...@googlemail.com: Thank you Justin. It helped but in my *top file I have still the old connection and the new ones. Can I simply delete connection I do not want? 2014-08-06 2:32 GMT+01:00 Justin Lemkul jalem...@vt.edu: On 8/5/14, 11:59 AM, Dawid das wrote: Dear Gromacs experts, I have found out why my force field does not work properly. I have added a new residue according to manual I found on Gromacs website. I modified all of the files. Now I have revealed that my new residue does not have connection to natural aminoacids in my topology file! If you take a look at it you will see that atoms 970 and 1009 are connected while the truth is that atoms 970 (carbonyl C atom of Phe65) and 1008 (MN1 atom of CH6 (new) residue) but also atoms 994 (MC3 atom of new residue) and 1009 (peptide N atom of Ser69) should be bonded. I have specified bonded parameters between those atom types in ffbonded.itp file but not in aminoacids.rtp. In other words my topology file does not recognize the connection between new residue and natural aminoacids residues. It seems like I do not specify something correctly in force field but I cannot find my mistake. Shall I specify this connection in specbond.dat file? You do not need specbond.dat. If the CH6 residue is an integral part of the protein backbone, you need to specify the inter-residue bonds using the +/- mechanism with appropriate atom names. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Any way to use GROMACS 4.6.x and 5 together
Dear Tamas and Mark,
Thank you for your help. Since I am using GROMACS 4.6.x and 5, the default
binary names are different, i.e., g_xxx versus gmx xxx, compiling with
different suffixes are not necessary. It seems Mark's idea is most
fault-proof, though sourcing different .bashrc files one at a time defeats
the my purpose of asking this question. Thank you guys anyway.
Regards,
Bin
2014-08-04 9:52 GMT-04:00 gromacs.org_gmx-users-requ...@maillist.sys.kth.se
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Today's Topics:
1. Re: Any way to use GROMACS 4.6.x and 5 together (Tamas Karpati)
2. Error in inflategro.pl (neha bharti)
3. Re: Any way to use GROMACS 4.6.x and 5 together (Mark Abraham)
4. Re: Any way to use GROMACS 4.6.x and 5 together (Tamas Karpati)
5. Re: Error with tabulated potential and tip4p water model
(Udaya Dahal)
6. Re: Output help (Victor Rosas Garcia)
--
Message: 1
Date: Mon, 4 Aug 2014 13:08:00 +0200
From: Tamas Karpati tkarp...@gmail.com
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Any way to use GROMACS 4.6.x and 5 together
Message-ID:
can5ox5p7mwbsir+jos13vux3pe_4xfkfoksutzdc8rmbncx...@mail.gmail.com
Content-Type: text/plain; charset=UTF-8
Dear Bin,
On Sat, Aug 2, 2014 at 12:44 PM, massimo sandal deviceran...@gmail.com
wrote:
Compile them with different suffixes? So that you have binaries like
mdrun_46 and mdrun_50 ?
Additional tip: if you don't want to rename all the executables
you may simply create a soft link to one of the install folders,
then -when need to change- remove it then re-create with the other one.
In detail: I have the following lines in my /home/myname/.bashrc:
export PATH=${PATH}:${HOME}/gromacs_bin/bin
export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${HOME}/gromacs_bin/lib
I have two (in fact more) compiled versions: gromacs-4.6.6_bin and
gromacs-5.0_bin. When I want to use the 4.6.6 version:
rm -f ~/gromacs_bin
ln -s ~/gromacs-4.6.6_bin ~/gromacs_bin
Then to switch to the other:
rm -f ~/gromacs_bin
ln -s ~/gromacs-5.0_bin ~/gromacs_bin
If you're in a unix shell, you need to re-open it for .bashrc to take
effect.
I assumed you're running GROMACS under some Linux/Unix platform
but probably the same can be achieved on any other OS.
Hope this helps,
t
On 2 Aug 2014 00:32, Bin Liu fdusuperstr...@gmail.com wrote:
Dear everyone,
I am having trouble with putting GROMACS 4.6.x and 5 together. If I put
these two lines in .bashrc file,
source /usr/local/gromacs4.6.5/bin/GMXRC
source /usr/local/gromacs5.0/bin/GMXRC
The second line will undo the work by the first line, i.e., I can use
only
gmx order of GROMACS 5 (for example), not g_order of GROMACS 4.6.5
Is there any way to let these two versions work together? Or I should
just
put both directories in the PATH environment variable? Thanks.
Cheers,
Bin
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Message: 2
Date: Mon, 4 Aug 2014 17:00:10 +0530
From: neha bharti nehabharty...@gmail.com
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Error in inflategro.pl
Message-ID:
cajtvtjcqwhbc_s_npbkgv8q6y3mfkhuw2u7fokpy4bprzpb...@mail.gmail.com
Content-Type: text/plain; charset=UTF-8
Hello All
I am trying to perform MD for protein ligand protein complex in popc lipid
with charmm36 force field and also follow Justin A. Lemkul tutorial.
I generated small molecule topology file from SwissParam which provides
.pdb file for ligand molecule.
I don't have .gro file for small molecule thats why I have created all the
file in .pdb
Re: [gmx-users] New residue in FF does not bond to others.
On 8/6/14, 12:04 PM, Dawid das wrote: Cause now what happens is that grompp requires bonding parameters for atoms which are actually bonded and for which are not (angle and dihedral parameters), e.g. CH6-Ser69 and CH6-Phe65 is what I want but I do not want connection between Ser69-Phe65. Now grompp asks me about bonding paramters for atoms which build all three residues while these residues are separated by more than 4 atoms. Properly constructed .rtp entries will not need manual editing, which is very error-prone. You're using lots of strange atom names, so you need to establish proper bonding from the CH6 residue; the +/- mechanism in flanking residues will fail. If you're getting connections between non-consecutive residues, that suggests a break in the chain when being processed by pdb2gmx; make sure CH6 is defined as a Protein residue in residuetypes.dat. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] New residue in FF does not bond to others.
These are lines that cause trouble: ERROR 1 [file mCherry7.top, line 18183]: No default U-B types ERROR 2 [file mCherry7.top, line 18250]: No default U-B types ERROR 3 [file mCherry7.top, line 25379]: No default Proper Dih. types ERROR 4 [file mCherry7.top, line 25380]: No default Proper Dih. types ERROR 5 [file mCherry7.top, line 25383]: No default Proper Dih. types ERROR 6 [file mCherry7.top, line 25386]: No default Proper Dih. types ERROR 7 [file mCherry7.top, line 25387]: No default Proper Dih. types ERROR 8 [file mCherry7.top, line 25388]: No default Proper Dih. types ERROR 9 [file mCherry7.top, line 25455]: No default Proper Dih. types ERROR 10 [file mCherry7.top, line 25457]: No default Proper Dih. types ERROR 11 [file mCherry7.top, line 25458]: No default Proper Dih. types Now in these files which I have already uploaded I have only added two extra lines just above [ angles ] section of CH6 residue in aminoacids.rtp (lines 1793 and 1794): MC3 +N 0.1345 154808.0 MN1 -C 0.139 173594.2 I have not changed anything else in any other file. Now the problem is that I have consecutive residues Phe65-CH6-Ser69. MN1 atom of CH6 is supposed to be bonded to C atom of Phe65. MC3 atom of CH6 is supposed to be bonded to atom NH1 of Ser69. C atom of Phe65 is not supposed to be bonded to NH1 atom of Ser69 but it is in my *top file. What other files do you need? Best wishes, Dawid Grabarek 2014-08-06 20:04 GMT+01:00 Justin Lemkul jalem...@vt.edu: On 8/6/14, 12:52 PM, Dawid das wrote: Yes CH6 is defined as a Protein. In fact pdb2gmx sees two chains. How to work it out then? You'll need to provide files and describe exactly what the problems are (lines in the topology, please) and what changes you have made since the last bundle of files you uploaded. -Justin 2014-08-06 19:45 GMT+01:00 Justin Lemkul jalem...@vt.edu: On 8/6/14, 12:04 PM, Dawid das wrote: Cause now what happens is that grompp requires bonding parameters for atoms which are actually bonded and for which are not (angle and dihedral parameters), e.g. CH6-Ser69 and CH6-Phe65 is what I want but I do not want connection between Ser69-Phe65. Now grompp asks me about bonding paramters for atoms which build all three residues while these residues are separated by more than 4 atoms. Properly constructed .rtp entries will not need manual editing, which is very error-prone. You're using lots of strange atom names, so you need to establish proper bonding from the CH6 residue; the +/- mechanism in flanking residues will fail. If you're getting connections between non-consecutive residues, that suggests a break in the chain when being processed by pdb2gmx; make sure CH6 is defined as a Protein residue in residuetypes.dat. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] gmx 4.6.6: rvdw == rcoulomb for Verlet lists
Good afternoon! When using the Verlet lists cut-off scheme, grompp will throw an error if the values for both *rcoulomb* and *rvdw* are not the same. However, when performing md with *mdrun* and *-tunepme yes*, the coulomb cutoff will be adjusted along with the pme grid to improve performance. If the coulomb cutoff must equal that used for vdw, is this also adjusted during the tuning? I ask because we are performing simulations with CHARMM36 lipids, and these have been shown to be sensitive to vdw cutoffs. Thanks! David -- David L. Dotson Center for Biological Physics Arizona State University Email: dldot...@asu.edu -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] pdb2gmx cannot generate the right residue and atom numbers
Thank you for your reply. I am just wondering is there anyway we can make pdb2gmx change the default digit number? I am doing a membrane protein, and I already have a ideal model as a pdb file. If I need to go over the solvate(or genbox in the 4.5.x version), by default waterbox setting the water will go into the lipid layer since the algorithm is just to put water into all the spaces, I may have to manually delete those water. If I can just transfer the model it will make life much easier and I can also compare with the known result. Thanks again for your time! In addition to what Joao said, the fixed-width .pdb format is fundamentally unsuited to large systems. You need to find a way to avoid using such a .pdb file as input to pdb2gmx; either solvate later, or use a different format for input. Mark On Mon, Aug 4, 2014 at 11:09 PM, WH signoreguid...@163.com wrote: Dear Gromacs users, I want to use Gromacs to process a system with more than 8 water moelcules. However, when use pdb2gmx to deal the the pdb file, the out put .gro file has the form like this: 3409HOHHW234995 -5.617 -6.883 -8.771 3409HOH OW34996 -6.108 -6.959 -7.760 3409HOHHW134997 -6.107 -6.973 -7.855 3409HOHHW234998 -6.199 -6.971 -7.735 3409HOH OW34999 -4.964 -8.455 -9.110 3409HOHHW135000 -5.054 -8.441 -9.081 3409HOHHW235001 -4.939 -8.372 -9.150 3409HOH OW35002 -6.157 -7.576 -8.913 3409HOHHW135003 -6.187 -7.499 -8.962 Only 4 digits will be used for the residue number and 5 for the atom number. Thus, the actual residue number and atom number cannot be written correctly and lead to failure for the MD simulation. Does anyone know how to fix this problem? I really appreciate it. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] New residue in FF does not bond to others.
On 8/6/14, 1:36 PM, Dawid das wrote: These are lines that cause trouble: ERROR 1 [file mCherry7.top, line 18183]: No default U-B types ERROR 2 [file mCherry7.top, line 18250]: No default U-B types ERROR 3 [file mCherry7.top, line 25379]: No default Proper Dih. types ERROR 4 [file mCherry7.top, line 25380]: No default Proper Dih. types ERROR 5 [file mCherry7.top, line 25383]: No default Proper Dih. types ERROR 6 [file mCherry7.top, line 25386]: No default Proper Dih. types ERROR 7 [file mCherry7.top, line 25387]: No default Proper Dih. types ERROR 8 [file mCherry7.top, line 25388]: No default Proper Dih. types ERROR 9 [file mCherry7.top, line 25455]: No default Proper Dih. types ERROR 10 [file mCherry7.top, line 25457]: No default Proper Dih. types ERROR 11 [file mCherry7.top, line 25458]: No default Proper Dih. types Now in these files which I have already uploaded I have only added two extra lines just above [ angles ] section of CH6 residue in aminoacids.rtp (lines 1793 and 1794): MC3 +N 0.1345 154808.0 MN1 -C 0.139 173594.2 I have not changed anything else in any other file. Now the problem is that I have consecutive residues Phe65-CH6-Ser69. MN1 atom of CH6 is supposed to be bonded to C atom of Phe65. MC3 atom of CH6 is supposed to be bonded to atom NH1 of Ser69. C atom of Phe65 is not supposed to be bonded to NH1 atom of Ser69 but it is in my *top file. What other files do you need? The same ones you provided before. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] gmx 4.6.6: rvdw == rcoulomb for Verlet lists
On 8/6/14, 3:56 PM, David Dotson wrote: Good afternoon! When using the Verlet lists cut-off scheme, grompp will throw an error if the values for both *rcoulomb* and *rvdw* are not the same. However, when performing md with *mdrun* and *-tunepme yes*, the coulomb cutoff will be adjusted along with the pme grid to improve performance. If the coulomb cutoff must equal that used for vdw, is this also adjusted during the tuning? I ask because we are performing simulations with CHARMM36 lipids, and these have been shown to be sensitive to vdw cutoffs. rvdw is not adjusted, just rcoulomb. The requirement for rcoulomb = rvdw is for grompp processing. It works the same way as rlist; it gets tuned during the run with the Verlet scheme. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] ligand binding
hello I have used charmm27 force field to parametrize my protein(human serum albumin,584a.a) and swiss param to provide parameters to the ligand due to which coordinates of ligand is changed and active site of protein is also completely changed. Can anybody tell me that ligand coordinates should be changed after parametrization? or any energy minimisation problem is there. Am i doing right or not? My energy minimization mdp file is here:- cpp= /lib/cpp include= -I../top integrator= steep emtol= 100 nsteps= 200 nstenergy= 10 nstxtcout= 10 xtc_grps= Protein energygrps= Protein nstlist= 5 ns_type= grid rlist= 1.4 coulombtype= PME rcoulomb= 1.4 rvdw= 1.4 constraints= none pbc= xyz Energy is not reached upto mentioned limit after EM run. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] gmx 4.6.6: rvdw == rcoulomb for Verlet lists
Thanks for the clear reply Justin. If *rvdw* does not change, that is enough for me. Out of curiosity, what is the technical reason for the requirement rcoulomb = rvdw, especially if rcoulomb is allowed to change during the simulation from tuning? David On 08/06/2014 06:28 PM, Justin Lemkul wrote: On 8/6/14, 3:56 PM, David Dotson wrote: Good afternoon! When using the Verlet lists cut-off scheme, grompp will throw an error if the values for both *rcoulomb* and *rvdw* are not the same. However, when performing md with *mdrun* and *-tunepme yes*, the coulomb cutoff will be adjusted along with the pme grid to improve performance. If the coulomb cutoff must equal that used for vdw, is this also adjusted during the tuning? I ask because we are performing simulations with CHARMM36 lipids, and these have been shown to be sensitive to vdw cutoffs. rvdw is not adjusted, just rcoulomb. The requirement for rcoulomb = rvdw is for grompp processing. It works the same way as rlist; it gets tuned during the run with the Verlet scheme. -Justin -- David L. Dotson Center for Biological Physics Arizona State University Email: dldot...@asu.edu -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] User-PME
Good idea. If my idea is right, then you should be able to change the table and observe that the reciprocal space part does not change... I would certainly look at what the potential is for systems for two atoms at a range of distances. Mark On Wed, Aug 6, 2014 at 11:44 AM, O'Neill, David d.o-ne...@warwick.ac.uk wrote: Mark, Thankyou for your response. Knowing this makes my life much easier, although I will of course run a test system to check. Regards, David From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Mark Abraham mark.j.abra...@gmail.com Sent: 06 August 2014 16:10 To: Discussion list for GROMACS users Subject: Re: [gmx-users] User-PME Hi, Haven't looked at the code, but the table maps to the real space part only, because it shares the implementation with the other kinds of user tables, for which reciprocal-space considerations do not apply. Mark On Wed, Aug 6, 2014 at 8:36 AM, O'Neill, David d.o-ne...@warwick.ac.uk wrote: Hello gromacs users, I have a question about the mdp option User-PME. I am right in saying that if I choose a potential for the electrostatics, f(r) in my user tables, it is just for the real space part of the Ewald sum and then User-PME calculates the reciprocal and self-correction terms? Or do I need to include these in the f(r) function in my user tables? Any help is much appreciated. Regards David -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
