[gmx-users] Claculating Equilibrium constants
Hello all, I have a protein bound to ions. is there a way to calculate the Kd of the bound ion in Gromaces so I can compare it to experimental Kd? Thanks, Gideon -- 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] Claculating Equilibrium constants
Hi Gideon, If the binding is relatively weak and the force field parameters are good enough that should be feasible. See e.g., Biophys J. 2005 August; 89(2): 768–781. However, in other cases this is more challenging. This is discussed in details for simulations of a Zinc binding protein in Phys Chem Chem Phys. 2009 Feb 14; 11(6): 975-83 Good luck, Ran Ran Friedman Biträdande Lektor (Assistant Professor) Linnaeus University School of Natural Sciences 391 82 Kalmar, Sweden +46 480 446 290 Telephone +46 76 207 8763 Mobile ran.fried...@lnu.se http://lnu.se/research-groups/computational-chemistry-and-biochemistry-group?l=en From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of גדעון לפידות [glapid...@gmail.com] Sent: 30 November 2010 10:45 To: gmx-users@gromacs.org Subject: [gmx-users] Claculating Equilibrium constants Hello all, I have a protein bound to ions. is there a way to calculate the Kd of the bound ion in Gromaces so I can compare it to experimental Kd? Thanks, Gideon -- 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] Looking for Gromacs test users
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[gmx-users] g_select / Input error or input inconsistency
Dear Teemu Murtola I study interaction of protein-dna in water. I want to obtain number of water molecule which are simultaneously closer than 3 A° from protein and DNA. my selection.dat file is as follows: waterO = group SOL and name OW; heavy1 = group Protein and group Protein-H; heavy2 = group DNA and group Protein-H; inter = waterO and within 0.3 of heavy1 and within 0.3 of heavy2; inter; when I use g-select -f .xtc -s .tpr -n .ndx -sf , selection parser: syntax error heavy1 = group Protein and group Protein-H' --- Program g_select, VERSION 4.5.1 Source code file: trajana.c, line: 1310 Input error or input inconsistency: selection(s) could not be parsed For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Am I doing it incorrect ? Is there problem in my .ndx file? Is this error a bug in gromacs 4.5.1? Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical Physical Chemistry Group -- 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] tfe.gro
Hi Hengameh Below, my TFE.gro (with the atom names for CHARMM Cgenff) i used it previously for md. You can easely translated in others ff you use 9 1TFE O11 0.397 1.386 1.484 0.4892 -0.3653 -0.3242 1TFEHO12 0.446 1.346 1.557 0.8382 -0.5070 -0.6322 1TFEH113 0.334 1.332 1.295 1.2033 -0.8553 -0.5343 1TFEH124 0.436 1.209 1.380 2.6521 2.1877 0.2597 1TFE C15 0.355 1.285 1.393 0. -0.4118 -0.0512 1TFEF216 0.186 1.128 1.352 0.1711 -0.0500 0.0270 1TFEF227 0.117 1.302 1.447 -0.1931 0.5088 -0.2066 1TFEF238 0.235 1.159 1.557 0.0214 0.0727 -0.2415 1TFE C29 0.224 1.222 1.439 -0.3522 0.2823 -0.0958 and the TFE.pdb file used to obtain the gro file above ATOM 1 O1 TFE 1 1.9123 -0.2235 0. ATOM 2 HO1 TFE 1 2.7589 0.2000 0. ATOM 3 H11 TFE 1 0.9282 1.3623 -0.8827 ATOM 4 H12 TFE 1 0.9282 1.3623 0.8827 ATOM 5 C1 TFE 1 -0.4189 0.0062 -0. ATOM 6 F21 TFE 1 -1.4055 0.8930 -0. ATOM 7 F22 TFE 1 -0.5650 -0.7556 -1.0660 ATOM 8 F23 TFE 1 -0.5650 -0.7556 1.0660 ATOM 9 C2 TFE 1 0.9031 0.7318 -0. Hope it helps Stefane winmail.dat-- 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] tfe.gro
Thank you very much ABEL Stephane. On Tue, Nov 30, 2010 at 3:28 PM, ABEL Stephane 175950 stephane.a...@cea.frwrote: Hi Hengameh Below, my TFE.gro (with the atom names for CHARMM Cgenff) i used it previously for md. You can easely translated in others ff you use 9 1TFE O11 0.397 1.386 1.484 0.4892 -0.3653 -0.3242 1TFEHO12 0.446 1.346 1.557 0.8382 -0.5070 -0.6322 1TFEH113 0.334 1.332 1.295 1.2033 -0.8553 -0.5343 1TFEH124 0.436 1.209 1.380 2.6521 2.1877 0.2597 1TFE C15 0.355 1.285 1.393 0. -0.4118 -0.0512 1TFEF216 0.186 1.128 1.352 0.1711 -0.0500 0.0270 1TFEF227 0.117 1.302 1.447 -0.1931 0.5088 -0.2066 1TFEF238 0.235 1.159 1.557 0.0214 0.0727 -0.2415 1TFE C29 0.224 1.222 1.439 -0.3522 0.2823 -0.0958 and the TFE.pdb file used to obtain the gro file above ATOM 1 O1 TFE 1 1.9123 -0.2235 0. ATOM 2 HO1 TFE 1 2.7589 0.2000 0. ATOM 3 H11 TFE 1 0.9282 1.3623 -0.8827 ATOM 4 H12 TFE 1 0.9282 1.3623 0.8827 ATOM 5 C1 TFE 1 -0.4189 0.0062 -0. ATOM 6 F21 TFE 1 -1.4055 0.8930 -0. ATOM 7 F22 TFE 1 -0.5650 -0.7556 -1.0660 ATOM 8 F23 TFE 1 -0.5650 -0.7556 1.0660 ATOM 9 C2 TFE 1 0.9031 0.7318 -0. Hope it helps Stefane -- 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 -- Hengameh Fallah M.Sc. Computational Chemistry -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_select / Input error or input inconsistency
leila karami wrote: Dear Teemu Murtola I study interaction of protein-dna in water. I want to obtain number of water molecule which are simultaneously closer than 3 A° from protein and DNA. my selection.dat file is as follows: waterO = group SOL and name OW; heavy1 = group Protein and group Protein-H; heavy2 = group DNA and group Protein-H; inter = waterO and within 0.3 of heavy1 and within 0.3 of heavy2; inter; when I use g-select -f .xtc -s .tpr -n .ndx -sf , selection parser: syntax error heavy1 = group Protein and group Protein-H' --- Program g_select, VERSION 4.5.1 Source code file: trajana.c, line: 1310 Input error or input inconsistency: selection(s) could not be parsed For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Am I doing it incorrect ? Is there problem in my .ndx file? I have never used g_select, but it seems to me there could be several problems. The group heavy1 is redundant - atoms that are in Protein and Protein-H will, by necessity, just be Protein-H. Perhaps the parser is complaining about the inconsistency in the lines - sometimes you have a group name enclosed in quotes and sometimes you do not. I doubt that heavy2 can be satisfied - how can an atom be in both DNA and Protein-H simultaneously? I think what you might want there is an or instead of and. You probably don't want a merged Protein-H/DNA group anyway, because then in your last line you are identifying any water O atom within 0.3 nm of any Protein-H or DNA atom, not those that are specifically between the two. -Justin Is this error a bug in gromacs 4.5.1? Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical Physical Chemistry Group -- 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] g_select / Input error or input inconsistency
Dear Justin thanks for your attention. 1) my system consists of protein, dna, and water. In my .ndx file, protein-H is all of non hydrogen atoms of protein and dna. it is my nomination for .ndx file. 2) I want to obtain number of water molecule which are simultaneously closer than 3 A° from protein and DNA* *and not protein or dna.* * * * -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical Physical Chemistry Group -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_select / Input error or input inconsistency
leila karami wrote: Dear Justin thanks for your attention. 1) my system consists of protein, dna, and water. In my .ndx file, protein-H is all of non hydrogen atoms of protein and dna. it is my nomination for .ndx file. Providing this kind of information up front would have been useful. It's also a bad idea. If Protein-H is actually all non-H protein and DNA atoms, you'll never achieve what you want. Use Gromacs' default group of Protein-H for what you want to do. Dealing with a single group of protein and DNA atoms (any subset) does not allow for the type of selection you need. 2) I want to obtain number of water molecule which are simultaneously closer than 3 A° from protein and DNA/ /and not protein or dna./ / I understand your objective. I stand by my previous comments. -Justin / / -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical Physical Chemistry Group -- 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] intra-chain peptide bond
Dear Gromacs Users: I was wondering if there is a way to introduce an intra-chain peptide bond between side chains of LYS1 and GLU30 of Pin1 WW domain (PDB ID: 1I6C, Model 1). I'm trying to check if additional stability can be acquired from cyclisation using MD simulation. The distance between NZ of LYS1 and CD of GLU30 is 3.3A. How can I make them to be close enough to form a peptide bond, and even if I manage to get them close enough, how can I actually introduce a peptide bond? Should I add modified residue information to somewhere? Thanks in advance! Best regards, Semin -- 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] intra-chain peptide bond
Semin Lee wrote: Dear Gromacs Users: I was wondering if there is a way to introduce an intra-chain peptide bond between side chains of LYS1 and GLU30 of Pin1 WW domain (PDB ID: 1I6C, Model 1). I'm trying to check if additional stability can be acquired from cyclisation using MD simulation. The distance between NZ of LYS1 and CD of GLU30 is 3.3A. How can I make them to be close enough to form a peptide bond, and even if I manage to get them close enough, how can I actually introduce a peptide bond? Should I add modified residue information to somewhere? You will need to: 1. Make custom residues in the .rtp file of the force field of interest (i.e., LYS with only one proton, GLU without the terminal O). 2. Modify specbond.dat to add the inter-residue bond. -Justin Thanks in advance! Best regards, Semin -- 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] intra-chain peptide bond
Justin A. Lemkul wrote: Semin Lee wrote: Dear Gromacs Users: I was wondering if there is a way to introduce an intra-chain peptide bond between side chains of LYS1 and GLU30 of Pin1 WW domain (PDB ID: 1I6C, Model 1). I'm trying to check if additional stability can be acquired from cyclisation using MD simulation. The distance between NZ of LYS1 and CD of GLU30 is 3.3A. How can I make them to be close enough to form a peptide bond, and even if I manage to get them close enough, how can I actually introduce a peptide bond? Should I add modified residue information to somewhere? You will need to: 1. Make custom residues in the .rtp file of the force field of interest (i.e., LYS with only one proton, GLU without the terminal O). ...and the relevant .hdb file to include your custom LYS residue, if needed. -Justin 2. Modify specbond.dat to add the inter-residue bond. -Justin Thanks in advance! Best regards, Semin -- 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] g_select / Input error or input inconsistency
Dear Justin I made new .ndx file in which there are following groups: protein protein-H DNA DNA-H SOL I changed selection.dat file to waterO = group SOL and name OW; heavy1 = group Protein-H; heavy2 = group DNA-H; inter = waterO and within 0.3 of heavy1 and within 0.3 of heavy2; inter; but again I encountered same error: selection parser: syntax error heavy1 = group Protein-H'selection ' --- Program g_select, VERSION 4.5.1 Source code file: trajana.c, line: 1310 Input error or input inconsistency: selection(s) could not be parsed For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_select / Input error or input inconsistency
leila karami wrote: Dear Justin I made new .ndx file in which there are following groups: protein protein-H DNA DNA-H SOL I changed selection.dat file to waterO = group SOL and name OW; heavy1 = group Protein-H; heavy2 = group DNA-H; inter = waterO and within 0.3 of heavy1 and within 0.3 of heavy2; inter; but again I encountered same error: selection parser: syntax error heavy1 = group Protein-H'selection ' You have to enclose the group name in quotes if it contains a symbol like '-' which, I think, is otherwise interpreted as subtraction. -Justin --- Program g_select, VERSION 4.5.1 Source code file: trajana.c, line: 1310 Input error or input inconsistency: selection(s) could not be parsed For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors -- 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] g_select / Input error or input inconsistency
Dear Justin I enclosed the group name Protein-H and DNA-H in quotes ' ' and . waterO = group SOL and name OW; heavy1 = group 'Protein-H'; heavy2 = group 'DNA-H'; inter = waterO and within 0.3 of heavy1 and within 0.3 of heavy2; inter; waterO = group SOL and name OW; heavy1 = group Protein-H; heavy2 = group DNA-H; inter = waterO and within 0.3 of heavy1 and within 0.3 of heavy2; inter; but in both of states again: selection parser: syntax error heavy1 = group 'Protein-H''lection ' --- Program g_select, VERSION 4.5.1 Source code file: trajana.c, line: 1310 Input error or input inconsistency: selection(s) could not be parsed For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical Physical Chemistry Group -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_select / Input error or input inconsistency
leila karami wrote: Dear Justin I enclosed the group name Protein-H and DNA-H in quotes ' ' and . waterO = group SOL and name OW; heavy1 = group 'Protein-H'; heavy2 = group 'DNA-H'; inter = waterO and within 0.3 of heavy1 and within 0.3 of heavy2; inter; waterO = group SOL and name OW; heavy1 = group Protein-H; heavy2 = group DNA-H; inter = waterO and within 0.3 of heavy1 and within 0.3 of heavy2; inter; but in both of states again: selection parser: syntax error heavy1 = group 'Protein-H''lection ' --- Program g_select, VERSION 4.5.1 Source code file: trajana.c, line: 1310 Please upgrade to version 4.5.3 and try again. The syntax I described above works correctly for me. -Justin Input error or input inconsistency: selection(s) could not be parsed For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical Physical Chemistry Group -- 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] Temporary downtime for git.gromacs.org Wednesday
Hi, We'll be moving git.gromacs.org to a new server room in a different building tomorrow, so it might be unavailable for a short while tomorrow afternoon European time. Sorry for the inconvenience! Cheers, Erik Sent from my iPhone-- 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] C6 attractive term off OPLSAA
I tried using the nonbonded parameters as defined below in my ffoplsaanb.itp file for methanol in water and this is the syntax I used: [nonbond_params ] ;i j funcc6 c12 opls_154opls_111 1 0.00E+000 2.43E-006 opls_154opls_112 1 0.00E+000 0.00E+000 opls_154opls_112 1 0.00E+000 0.00E+000 opls_155opls_111 1 0.00E+000 0.00E+000 opls_155opls_112 1 0.00E+000 0.00E+000 opls_155opls_112 1 0.00E+000 0.00E+000 opls_156opls_111 1 0.00E+000 2.70E-007 opls_156opls_112 1 0.00E+000 0.00E+000 opls_156opls_112 1 0.00E+000 0.00E+000 opls_157opls_111 1 0.00E+000 3.01E-006 opls_157opls_112 1 0.00E+000 0.00E+000 When I tried to do mdrun, I got an error saying my system is exploding. I tried doing the mdrun without nonbonded parameters and it runs fine. So I am not sure if I am using the nonbond_params concept correctly. i.e. I want C6 to be zero between my solute (methanol) and solvent (water). This is the error: Warning: 1-4 interaction between 2 and 6 at distance 3.786 which is larger than the 1-4 table size 2.500 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size Suggestions? Thanks. -Nisha P Quoting nishap.pa...@utoronto.ca: Okay I am going to give it a try. I just wanted to make sure I was calculating C6 and C12 correctly as well using sigma and epsilon according to rule 3 C12 = Sigma^(6)*C6 C6 = 4*sigma^(6)*epsilon Thanks Quoting Justin A. Lemkul jalem...@vt.edu: nishap.pa...@utoronto.ca wrote: Hello, I have a concern regarding C6 attractive term in LJ potential. I am using OPLS-AA force field, and I wish to turn off attractive term C6 by setting the parameters to zero. One of the suggestion was to add a [nonbond_params] in my ffoplsaanb.itp file and set the C6 to zero between the non-bonded pair. In my system for example, which consists of one methanol in water, I wish to set C6 term to zero between my solute and solvent. Since OPLSAA is all atom force field it treats each atom individually and has sigma and epsilon for each atom, so I am not sure how I would actually set my nonbond_params in my nb.itp file. I realize I need to convert each sigma and epsilon to C6 and C12, so say for example for methanol in water my [nonbond_params] would look something like this? [ nonbond_params ] ; ij func c6 c12 CTOW 1 0.00 calculated value for C12 here? CTHW1 1 0.00 CTHW2 1 0.00 CT is the carbon in Methanol. OW, HW1 an HW2 correspond to atoms in TIP3P water model Is that correct? Would I have to do that for each atom in methanol? Sounds about right to me. -Justin Any suggestions would be appreciated. Thanks. Nisha P -- 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 mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_select / Input error or input inconsistency
On Tue, Nov 30, 2010 at 16:58, leila karami karami.lei...@gmail.com wrote: I enclosed the group name Protein-H and DNA-H in quotes ' ' and . You should use double quotes, but that does not appear to be the source of your problems. but in both of states again: selection parser: syntax error heavy1 = group 'Protein-H''lection ' If this really is the literal output from the tool, it appears that you have Windows-style line endings in the input selection file. Removing those should help. If I find the time at some point, I can try to make them work as well. Teemu -- 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] C6 attractive term off OPLSAA
nishap.pa...@utoronto.ca wrote: I tried using the nonbonded parameters as defined below in my ffoplsaanb.itp file for methanol in water and this is the syntax I used: [nonbond_params] ;ijfuncc6c12 opls_154opls_11110.00E+0002.43E-006 opls_154opls_11210.00E+0000.00E+000 opls_154opls_112 10.00E+0000.00E+000 opls_155opls_111 10.00E+0000.00E+000 opls_155opls_112 10.00E+0000.00E+000 opls_155opls_112 10.00E+0000.00E+000 opls_156opls_111 10.00E+0002.70E-007 opls_156opls_112 10.00E+0000.00E+000 opls_156opls_11210.00E+0000.00E+000 opls_157opls_111 10.00E+0003.01E-006 opls_157opls_112 10.00E+0000.00E+000 When I tried to do mdrun, I got an error saying my system is exploding. I tried doing the mdrun without nonbonded parameters and it runs fine. So I am not sure if I am using the nonbond_params concept correctly. i.e. I want C6 to be zero between my solute (methanol) and solvent (water). This is the error: Warning: 1-4 interaction between 2 and 6 at distance 3.786 which is larger than the 1-4 table size 2.500 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size Suggestions? Your implementation of your concept is technically correct, but perhaps physically unreasonable. You're turning off the attractive LJ component and leaving only a repulsive component. It sounds about right that everything is flying apart. -Justin Thanks. -Nisha P Quoting nishap.pa...@utoronto.ca: Okay I am going to give it a try. I just wanted to make sure I was calculating C6 and C12 correctly as well using sigma and epsilon according to rule 3 C12 = Sigma^(6)*C6 C6 = 4*sigma^(6)*epsilon Thanks Quoting Justin A. Lemkul jalem...@vt.edu: nishap.pa...@utoronto.ca wrote: Hello, I have a concern regarding C6 attractive term in LJ potential. I am using OPLS-AA force field, and I wish to turn off attractive term C6 by setting the parameters to zero. One of the suggestion was to add a [nonbond_params] in my ffoplsaanb.itp file and set the C6 to zero between the non-bonded pair. In my system for example, which consists of one methanol in water, I wish to set C6 term to zero between my solute and solvent. Since OPLSAA is all atom force field it treats each atom individually and has sigma and epsilon for each atom, so I am not sure how I would actually set my nonbond_params in my nb.itp file. I realize I need to convert each sigma and epsilon to C6 and C12, so say for example for methanol in water my [nonbond_params] would look something like this? [ nonbond_params ] ; ij func c6 c12 CTOW 1 0.00 calculated value for C12 here? CTHW1 1 0.00 CTHW2 1 0.00 CT is the carbon in Methanol. OW, HW1 an HW2 correspond to atoms in TIP3P water model Is that correct? Would I have to do that for each atom in methanol? Sounds about right to me. -Justin Any suggestions would be appreciated. Thanks. Nisha P -- 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 -- 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] Ions and charge groups
Hi everybody, Sorry about this, but I'm pretty new to gromacs and I couldn't find any clue about my problem in the archives or in the manual. I'm using gromacs 4.5.1, and my system is a rather big system (about 12x12x12) that includes a proteon, an atp molecule, water and some ions. I am using ffamber99sb force field. Now, I post the log for my mdrun. Initializing Domain Decomposition on 2 nodes Dynamic load balancing: auto Will sort the charge groups at every domain (re)decomposition Initial maximum inter charge-group distances: two-body bonded interactions: 14.813 nm, LJ-14, atoms 25682 25685 multi-body bonded interactions: 14.813 nm, Angle, atoms 25685 25686 Minimum cell size due to bonded interactions: 16.294 nm Using 0 separate PME nodes Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25 Optimizing the DD grid for 2 cells with a minimum initial size of 20.368 nm The maximum allowed number of cells is: X 0 Y 0 Z 0 --- Program mdrun, VERSION 4.5.1 Source code file: domdec.c, line: 6428 Fatal error: There is no domain decomposition for 2 nodes that is compatible with the given box and a minimum cell size of 20.368 nm Change the number of nodes or mdrun option -rdd or -dds Look in the log file for details on the domain decomposition For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Of course the main point here is this Initial maximum inter charge-group distances: two-body bonded interactions: 14.813 nm, LJ-14, atoms 25682 25685 multi-body bonded interactions: 14.813 nm, Angle, atoms 25685 25686 but they're CL ions! Why should they have any bonded interaction or angle interaction?? Actually, I made some tests, and: 1- if I solvate the protein+atp+ions (I want the ions to be in specific positions) system I get that 14nm bond error when I run mdrun, but grompp let it go. 2- in this situation, if I move in the gro file the coords for the ions after the water, same happens but now grompp throws a warning about charge group distance. 3- if I solvate then use genion to include the ions at least the simulation starts. Then I get this error A charge group moved too far between two domain decomposition steps, but that is probably related to my system I really don't get what's going on here. Thank you in advance for any feedback. Guido -- 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] Ions and charge groups
Guido Polles wrote: Hi everybody, Sorry about this, but I'm pretty new to gromacs and I couldn't find any clue about my problem in the archives or in the manual. I'm using gromacs 4.5.1, and my system is a rather big system (about 12x12x12) that includes a proteon, an atp molecule, water and some ions. I am using ffamber99sb force field. Now, I post the log for my mdrun. Initializing Domain Decomposition on 2 nodes Dynamic load balancing: auto Will sort the charge groups at every domain (re)decomposition Initial maximum inter charge-group distances: two-body bonded interactions: 14.813 nm, LJ-14, atoms 25682 25685 multi-body bonded interactions: 14.813 nm, Angle, atoms 25685 25686 Minimum cell size due to bonded interactions: 16.294 nm Using 0 separate PME nodes Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25 Optimizing the DD grid for 2 cells with a minimum initial size of 20.368 nm The maximum allowed number of cells is: X 0 Y 0 Z 0 --- Program mdrun, VERSION 4.5.1 Source code file: domdec.c, line: 6428 Fatal error: There is no domain decomposition for 2 nodes that is compatible with the given box and a minimum cell size of 20.368 nm Change the number of nodes or mdrun option -rdd or -dds Look in the log file for details on the domain decomposition For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Of course the main point here is this Initial maximum inter charge-group distances: two-body bonded interactions: 14.813 nm, LJ-14, atoms 25682 25685 multi-body bonded interactions: 14.813 nm, Angle, atoms 25685 25686 but they're CL ions! Why should they have any bonded interaction or angle interaction?? They shouldn't. Check your [bonds] and [angles] directives for these atom numbers. Apparently mdrun is finding bonds to these ions in your topology. Were these ions added with genion? Present in the initial structure processed by pdb2gmx? Manually added in some location? Actually, I made some tests, and: 1- if I solvate the protein+atp+ions (I want the ions to be in specific positions) system I get that 14nm bond error when I run mdrun, but grompp let it go. OK, so you want ions in specific positions. Did you put them there? If so, was it before or after you generated the topology (presumably with pdb2gmx)? 2- in this situation, if I move in the gro file the coords for the ions after the water, same happens but now grompp throws a warning about charge group distance. That's probably related to the contents of your .mdp file, which you haven't posted. It may or may not be related to the problem at hand. 3- if I solvate then use genion to include the ions at least the simulation starts. Then I get this error A charge group moved too far between two domain decomposition steps, but that is probably related to my system That error message indicates your system has become unstable, likely due to insufficient energy minimization or equilibration, or incorrect .mdp settings. http://www.gromacs.org/Documentation/Terminology/Blowing_Up -Justin I really don't get what's going on here. Thank you in advance for any feedback. Guido -- 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] Ions and charge groups
Justin A. Lemkul wrote: Guido Polles wrote: Hi everybody, Sorry about this, but I'm pretty new to gromacs and I couldn't find any clue about my problem in the archives or in the manual. I'm using gromacs 4.5.1, and my system is a rather big system (about 12x12x12) that includes a proteon, an atp molecule, water and some ions. I am using ffamber99sb force field. Now, I post the log for my mdrun. Initializing Domain Decomposition on 2 nodes Dynamic load balancing: auto Will sort the charge groups at every domain (re)decomposition Initial maximum inter charge-group distances: two-body bonded interactions: 14.813 nm, LJ-14, atoms 25682 25685 multi-body bonded interactions: 14.813 nm, Angle, atoms 25685 25686 Minimum cell size due to bonded interactions: 16.294 nm Using 0 separate PME nodes Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25 Optimizing the DD grid for 2 cells with a minimum initial size of 20.368 nm The maximum allowed number of cells is: X 0 Y 0 Z 0 --- Program mdrun, VERSION 4.5.1 Source code file: domdec.c, line: 6428 Fatal error: There is no domain decomposition for 2 nodes that is compatible with the given box and a minimum cell size of 20.368 nm Change the number of nodes or mdrun option -rdd or -dds Look in the log file for details on the domain decomposition For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Of course the main point here is this Initial maximum inter charge-group distances: two-body bonded interactions: 14.813 nm, LJ-14, atoms 25682 25685 multi-body bonded interactions: 14.813 nm, Angle, atoms 25685 25686 but they're CL ions! Why should they have any bonded interaction or angle interaction?? They shouldn't. Check your [bonds] and [angles] directives for these atom numbers. Apparently mdrun is finding bonds to these ions in your topology. Were these ions added with genion? Present in the initial structure processed by pdb2gmx? Manually added in some location? Actually, I made some tests, and: 1- if I solvate the protein+atp+ions (I want the ions to be in specific positions) system I get that 14nm bond error when I run mdrun, but grompp let it go. OK, so you want ions in specific positions. Did you put them there? If so, was it before or after you generated the topology (presumably with pdb2gmx)? Also relevant here, but I forgot to ask: are you using distance restraints to keep these ions in place? If so, that's your problem. If the restraints can't be placed in the same DD cell, you have to use particle decomposition (mdrun -pd), which is somewhat slower. -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] A warning concerning file ffnonbonded.itp overriding atomtype OT
Dear Gromacs society, I was running a simulation using CHARMM27/TIP3P/virtual sites. Gromacs version: 4.5.2 I had only one warning which says (file ffnonbonded.itp, line 68): overriding atomtype OT In the .gro and .top files produced by pdb2gmx, the only atoms that are described as OT are the two oxygen atoms of the C-terminal carboxylic acid group (neutral in my system), they are assigned as OT1 and OT2...No other oxygen atom is described as OT First questions: How harmful this warning could be to the integrity of my simulation? I would assume it shouldn't be that harmful because my system has a fairly big, well folded protein (331 residues) and the C-terminus is far far away from the area I am interested in, besides the overriding itself imply a corrective action by gromacs!!! Second issue: while I am searching the web for the above issue, I camE across this website: http://towhee.sourceforge.net/forcefields/charmm27.html http://towhee.sourceforge.net/forcefields/charmm27.html If you go all the way down to the section of Oxygen atom descriptions, you will find that OT has the description of ( Water oxygen, modified TIP3P model). Well, this is weird because the carboxylate oxygens in the C-terminal COOH group were assigned as OT1 and OT2 whereas thay should have been assigned as OC1 and OC2 (OC is Carboxylate oxygen non-lipid version as mentioned in the same website)... I changed the OT1 and OT2 designations in the .top and .gro files to OC1 and OC2 and repeat the simulation, I unexpectedly still get the above warning message... now it is really confusing and that's why I decided to seek help from the gromacs mailist Any help, feedback, clarification is very much appreciated Great regards Hassan Shallal University of the Pacific, CA -- 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] A warning concerning file ffnonbonded.itp overriding atomtype OT
Hassan Shallal wrote: Dear Gromacs society, I was running a simulation using CHARMM27/TIP3P/virtual sites. Gromacs version: 4.5.2 I had only one warning which says *(file ffnonbonded.itp, line 68): overriding atomtype OT* In the .gro and .top files produced by pdb2gmx, the only atoms that are described as OT are the two oxygen atoms of the C-terminal carboxylic acid group (neutral in my system), they are assigned as OT1 and OT2...No other oxygen atom is described as OT First questions: How harmful this warning could be to the integrity of my simulation? I would assume it shouldn't be that harmful because my system has a fairly big, well folded protein (331 residues) and the C-terminus is far far away from the area I am interested in, besides the overriding itself imply a corrective action by gromacs!!! Second issue: while I am searching the web for the above issue, I camE across this website: http://towhee.sourceforge.net/forcefields/charmm27.html If you go all the way down to the section of Oxygen atom descriptions, you will find that *OT* has the description of (* Water oxygen, modified TIP3P model).* Well, this is weird because the carboxylate oxygens in the C-terminal COOH group were assigned as OT1 and OT2 whereas thay should have been assigned as OC1 and OC2 (*OC is Carboxylate oxygen non-lipid version* as mentioned in the same website)... I changed the OT1 and OT2 designations in the .top and .gro files to OC1 and OC2 and repeat the simulation, I unexpectedly still get the above warning message... now it is really confusing and that's why I decided to seek help from the gromacs mailist Any help, feedback, clarification is very much appreciated Atom types (in the force field files and topology) and atom names (in the coordinate file) are different. Your error has nothing to do with your C-terminal carboxylate. Apparently, you're trying to use a heavy water model, since line 68 of ffnonbonded is: 66 OT 8 15.999400 -0.834 A 0.315057422683 0.6363864 67 #ifdef HEAVY_H 68 OT 8 9.951400-0.834 A 0.315057422683 0.6363864 ; CHARMM TIP3p O 69 #endif The normal OT type is on line 66, but is being overridden by a define statement. -Justin Great regards Hassan Shallal University of the Pacific, CA -- 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] Large Periodic Molecule
Hi all, I am having a problem, where my simulation fails when I run on multiple nodes. On an 8-core machine, my job runs fine, but when I run on 240 processors (20 12-core nodes), I get the errors U-B of 59312 missing 1 followed by Software inconsistency error: Some interactions seem to be assigned multiple times I can use the .tpr file from the supercomputer (the 240 core job) and it runs fine on my 8-core machine as well. I believe the problem is that I am simulating a system containing an infinite slab of amorphous silica, which is one large molecule, bonded to itself across the periodic boundaries. I am using the charmm-compatible parameters developed by Cruz-Chu, Aksimentiev and Schulten (http://www.ks.uiuc.edu/Research/silica/SiO2ff.html), so I have each atom as its own charge group, and each atom is harmonically restrained to its initial coordinates (I also added in angle terms with small force constants so that I could use the GBSA solver, which requires all bonded triplets to have an angle defined). From my discussions with others, I have heard that it is common to have such problems with infinite molecules, where not all information about bonded interactions are shared between nodes. One solution might be to use the old particle decomposition parallelization, but I would like to use domain decomposition for its speed. Has anyone had any experience with this? Thanks, Rogan -- 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] VDW radious (Gideon)
Hi all, General question, what is the significance of the VDW radious in the mdp files? for instance switching from 1.0 to 1.2, Thanks, -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Trouble with Gromacs finding the files it needs
Hello Gromacs users, I am having some difficulties with Gromacs finding the files it needs (at least that is what I *think* is the problem) and am hoping that someone can offer some insight. Using another user's home directory installation of Gromacs (v 4.0.7) I was able to work my way through Justin Lemkul's very nice lysozyme tutorial. However, now that I am working from my own home directory installation of Gromacs (v 4.5.3) I keep running into problems involving the addition of chloride ions in that same tutorial (as well as in other applications). The error I'm receiving using the newer version and installation of Gromacs occurs when I am using grommp to prepare a file containing protein, solvent, and ions for energy minimization: --- Program grompp, VERSION 4.5.3 Source code file: toppush.c, line: 1987 Fatal error: No such moleculetype CL- For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- This is very confusing since all I am doing is using a newer installation of Gromacs and following the exact same commands from the tutorial. Naturally I started checking and comparing topology files from the 2 runs to see if I could figure out what was going on. I noticed a few differences but am unsure what to make of them. The older version of Gromacs, for instance, has the user and host names correct at the top of the topology file, whereas my freshly installed version has both user and host as onbekend, so it seems that user and host information is not being communicated in my new copy of Gromacs. Also, the topology file generated by the older version has includes of the form of #include ffoplsaa.itp, #include posre.itp, #include spce.itp, and #include ions.itp whereas the newer version has includes of the form #include oplsaa.ff/forcefield.itp, #include posre.itp, #include oplsaa.ff/spce.itp, and #include oplsaa.ff/ions.itp. I know of course that CL- is the correct form of the chloride ion in OPLSAA (I checked oplsaa.ff/ions.itp to be certain), so I am quite baffled as to why this error is occurring. Is this indeed some sort of path problem, perhaps? I have noted that when I use CL instead of CL- in genion grommp has no trouble, but I believe it *should* because I have selected the OPLSAA forcefield. I have also noted that when I replace oplsaa.ff/ions.itp in my topology file with just ions.itp grommp runs fine, but this worries because I don't know why it works. In case it makes any difference, I installed Gromacs using the following procedure to yield MPI single and double precision versions of mdrun and single and double precision non-MPI versions of the tools: ./configure --enable-mpi --disable-float --prefix=/home/scott/gromacs --program-suffix=_mpi_d make mdrun make install-mdrun make distclean ./configure --enable-mpi --enable-float --prefix=/home/scott/gromacs --program-suffix=_mpi make mdrun make install-mdrun make distclean ./configure --disable-float --prefix=/home/scott/gromacs --program-suffix=_d make make install make distclean ./configure --enable-float --prefix=/home/scott/gromacs make make install Thank you very much for any help you can provide, this problem really has me scratching my head! -- J. Nathan Scott, Ph.D. Postdoctoral Fellow Department of Chemistry and Biochemistry Montana State University -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Trouble with Gromacs finding the files it needs
J. Nathan Scott wrote: Hello Gromacs users, I am having some difficulties with Gromacs finding the files it needs (at least that is what I *think* is the problem) and am hoping that someone can offer some insight. Using another user's home directory installation of Gromacs (v 4.0.7) I was able to work my way through Justin Lemkul's very nice lysozyme tutorial. However, now that I am working from my own home directory installation of Gromacs (v 4.5.3) I keep running into problems involving the addition of chloride ions in that same tutorial (as well as in other applications). The error I'm receiving using the newer version and installation of Gromacs occurs when I am using grommp to prepare a file containing protein, solvent, and ions for energy minimization: --- Program grompp, VERSION 4.5.3 Source code file: toppush.c, line: 1987 Fatal error: No such moleculetype CL- For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- This is very confusing since all I am doing is using a newer installation of Gromacs and following the exact same commands from the tutorial. Naturally I started checking and comparing topology files from the 2 runs to see if I could figure out what was going on. I noticed a few differences but am unsure what to make of them. The older version of Gromacs, for instance, has the user and host names correct at the top of the topology file, whereas my freshly installed version has both user and host as onbekend, so it seems that user and host information is not being communicated in my new copy of Gromacs. Also, the topology file generated by the older version has includes of the form of #include ffoplsaa.itp, #include posre.itp, #include spce.itp, and #include ions.itp whereas the newer version has includes of the form #include oplsaa.ff/forcefield.itp, #include posre.itp, #include oplsaa.ff/spce.itp, and #include oplsaa.ff/ions.itp. I know of course that CL- is the correct form of the chloride ion in OPLSAA (I checked oplsaa.ff/ions.itp to be certain), so I am quite baffled as to why this error is occurring. Is this indeed some sort of path problem, perhaps? I have noted that when I use CL instead of CL- in genion grommp has no trouble, but I believe it *should* because I have selected the OPLSAA forcefield. I have also noted that when I replace oplsaa.ff/ions.itp in my topology file with just ions.itp grommp runs fine, but this worries because I don't know why it works. The directory structure has changed as of version 4.5, and ion names have been standardized across the force fields. The proper [moleculetype] of the chloride ion (in oplsaa.ff/ions.itp) is indeed CL while the *residue name* is CL- and the atom name (which is what you pass to genion) is CL. So, if you have added a line like CL- 8 in the [molecules] directive of your topology (like in my tutorial), then you get the fatal error. The [moleculetype] name is what you enter here, not the residue name. I haven't updated my tutorial for version 4.5.x, but perhaps I should. If you follow what I say exactly, you will have problems in the newer version. -Justin In case it makes any difference, I installed Gromacs using the following procedure to yield MPI single and double precision versions of mdrun and single and double precision non-MPI versions of the tools: ./configure --enable-mpi --disable-float --prefix=/home/scott/gromacs --program-suffix=_mpi_d make mdrun make install-mdrun make distclean ./configure --enable-mpi --enable-float --prefix=/home/scott/gromacs --program-suffix=_mpi make mdrun make install-mdrun make distclean ./configure --disable-float --prefix=/home/scott/gromacs --program-suffix=_d make make install make distclean ./configure --enable-float --prefix=/home/scott/gromacs make make install Thank you very much for any help you can provide, this problem really has me scratching my head! -- J. Nathan Scott, Ph.D. Postdoctoral Fellow Department of Chemistry and Biochemistry Montana State University -- 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] VDW radious (Gideon)
גדעון לפידות wrote: Hi all, General question, what is the significance of the VDW radious in the mdp files? for instance switching from 1.0 to 1.2, Thanks, Cutoff radii are often considered part of the force field and should not be changed ad hoc. Coulombic cutoffs are less sensitive to such effects when using PME, but for rvdw, the effects can be dramatic, depending on the system. For instance, lipid bilayer properties can be significantly influenced by altering the value of rvdw. Refer to the primary literature of your force field for an appropriate setting, and do not deviate from it unless you can prove there is no deleterious effects (or someone else has already published such information). -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] Trouble with Gromacs finding the files it needs
On Tue, Nov 30, 2010 at 2:13 PM, Justin A. Lemkul jalem...@vt.edu wrote: J. Nathan Scott wrote: Hello Gromacs users, I am having some difficulties with Gromacs finding the files it needs (at least that is what I *think* is the problem) and am hoping that someone can offer some insight. Using another user's home directory installation of Gromacs (v 4.0.7) I was able to work my way through Justin Lemkul's very nice lysozyme tutorial. However, now that I am working from my own home directory installation of Gromacs (v 4.5.3) I keep running into problems involving the addition of chloride ions in that same tutorial (as well as in other applications). The error I'm receiving using the newer version and installation of Gromacs occurs when I am using grommp to prepare a file containing protein, solvent, and ions for energy minimization: --- Program grompp, VERSION 4.5.3 Source code file: toppush.c, line: 1987 Fatal error: No such moleculetype CL- For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- This is very confusing since all I am doing is using a newer installation of Gromacs and following the exact same commands from the tutorial. Naturally I started checking and comparing topology files from the 2 runs to see if I could figure out what was going on. I noticed a few differences but am unsure what to make of them. The older version of Gromacs, for instance, has the user and host names correct at the top of the topology file, whereas my freshly installed version has both user and host as onbekend, so it seems that user and host information is not being communicated in my new copy of Gromacs. Also, the topology file generated by the older version has includes of the form of #include ffoplsaa.itp, #include posre.itp, #include spce.itp, and #include ions.itp whereas the newer version has includes of the form #include oplsaa.ff/forcefield.itp, #include posre.itp, #include oplsaa.ff/spce.itp, and #include oplsaa.ff/ions.itp. I know of course that CL- is the correct form of the chloride ion in OPLSAA (I checked oplsaa.ff/ions.itp to be certain), so I am quite baffled as to why this error is occurring. Is this indeed some sort of path problem, perhaps? I have noted that when I use CL instead of CL- in genion grommp has no trouble, but I believe it *should* because I have selected the OPLSAA forcefield. I have also noted that when I replace oplsaa.ff/ions.itp in my topology file with just ions.itp grommp runs fine, but this worries because I don't know why it works. The directory structure has changed as of version 4.5, and ion names have been standardized across the force fields. The proper [moleculetype] of the chloride ion (in oplsaa.ff/ions.itp) is indeed CL while the *residue name* is CL- and the atom name (which is what you pass to genion) is CL. So, if you have added a line like CL- 8 in the [molecules] directive of your topology (like in my tutorial), then you get the fatal error. The [moleculetype] name is what you enter here, not the residue name. I haven't updated my tutorial for version 4.5.x, but perhaps I should. If you follow what I say exactly, you will have problems in the newer version. -Justin Ahhh, now it all makes sense! Thanks very much for your helpful answer Justin! By the way, should I be concerned about onbekend in the user and server names? I don't particularly care what is in those fields, but am slightly worried that they indicate I have something configured incorrectly, which could then affect the functionality of the software. -Nathan In case it makes any difference, I installed Gromacs using the following procedure to yield MPI single and double precision versions of mdrun and single and double precision non-MPI versions of the tools: ./configure --enable-mpi --disable-float --prefix=/home/scott/gromacs --program-suffix=_mpi_d make mdrun make install-mdrun make distclean ./configure --enable-mpi --enable-float --prefix=/home/scott/gromacs --program-suffix=_mpi make mdrun make install-mdrun make distclean ./configure --disable-float --prefix=/home/scott/gromacs --program-suffix=_d make make install make distclean ./configure --enable-float --prefix=/home/scott/gromacs make make install Thank you very much for any help you can provide, this problem really has me scratching my head! -- J. Nathan Scott, Ph.D. Postdoctoral Fellow Department of Chemistry and Biochemistry Montana State University -- 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
Re: [gmx-users] Trouble with Gromacs finding the files it needs
J. Nathan Scott wrote: snip Ahhh, now it all makes sense! Thanks very much for your helpful answer Justin! By the way, should I be concerned about onbekend in the user and server names? I don't particularly care what is in those fields, but am slightly worried that they indicate I have something configured incorrectly, which could then affect the functionality of the software. There's no problem. That's a default name specified in src/gmxlib/string2.c that is used in place of other parameters if they are not available. -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] Trouble with Gromacs finding the files it needs
Hi all, I believe onbekend is Dutch for unknown. Rogan On Nov 30, 2010, at 3:54 PM, Justin A. Lemkul wrote: J. Nathan Scott wrote: snip Ahhh, now it all makes sense! Thanks very much for your helpful answer Justin! By the way, should I be concerned about onbekend in the user and server names? I don't particularly care what is in those fields, but am slightly worried that they indicate I have something configured incorrectly, which could then affect the functionality of the software. There's no problem. That's a default name specified in src/gmxlib/ string2.c that is used in place of other parameters if they are not available. -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 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] C6 attractive term off OPLSAA
On 1/12/2010 5:06 AM, Justin A. Lemkul wrote: nishap.pa...@utoronto.ca wrote: I tried using the nonbonded parameters as defined below in my ffoplsaanb.itp file for methanol in water and this is the syntax I used: [nonbond_params] ;ijfuncc6c12 opls_154opls_11110.00E+0002.43E-006 opls_154opls_11210.00E+0000.00E+000 opls_154opls_112 10.00E+0000.00E+000 opls_155opls_111 10.00E+0000.00E+000 opls_155opls_112 10.00E+0000.00E+000 opls_155opls_112 10.00E+0000.00E+000 opls_156opls_111 10.00E+0002.70E-007 opls_156opls_112 10.00E+0000.00E+000 opls_156opls_11210.00E+0000.00E+000 opls_157opls_111 10.00E+0003.01E-006 opls_157opls_112 10.00E+0000.00E+000 When I tried to do mdrun, I got an error saying my system is exploding. I tried doing the mdrun without nonbonded parameters and it runs fine. So I am not sure if I am using the nonbond_params concept correctly. i.e. I want C6 to be zero between my solute (methanol) and solvent (water). This is the error: Warning: 1-4 interaction between 2 and 6 at distance 3.786 which is larger than the 1-4 table size 2.500 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size Suggestions? Your implementation of your concept is technically correct, but perhaps physically unreasonable. You're turning off the attractive LJ component and leaving only a repulsive component. It sounds about right that everything is flying apart. Indeed. The way to do this is with mdrun -rerun on a trajectory generated with the normal version of the forcefield, as I think I said in another thread yesterday. Mark -Justin Thanks. -Nisha P Quoting nishap.pa...@utoronto.ca: Okay I am going to give it a try. I just wanted to make sure I was calculating C6 and C12 correctly as well using sigma and epsilon according to rule 3 C12 = Sigma^(6)*C6 C6 = 4*sigma^(6)*epsilon Thanks Quoting Justin A. Lemkul jalem...@vt.edu: nishap.pa...@utoronto.ca wrote: Hello, I have a concern regarding C6 attractive term in LJ potential. I am using OPLS-AA force field, and I wish to turn off attractive term C6 by setting the parameters to zero. One of the suggestion was to add a [nonbond_params] in my ffoplsaanb.itp file and set the C6 to zero between the non-bonded pair. In my system for example, which consists of one methanol in water, I wish to set C6 term to zero between my solute and solvent. Since OPLSAA is all atom force field it treats each atom individually and has sigma and epsilon for each atom, so I am not sure how I would actually set my nonbond_params in my nb.itp file. I realize I need to convert each sigma and epsilon to C6 and C12, so say for example for methanol in water my [nonbond_params] would look something like this? [ nonbond_params ] ; ij func c6 c12 CTOW 1 0.00 calculated value for C12 here? CTHW1 1 0.00 CTHW2 1 0.00 CT is the carbon in Methanol. OW, HW1 an HW2 correspond to atoms in TIP3P water model Is that correct? Would I have to do that for each atom in methanol? Sounds about right to me. -Justin Any suggestions would be appreciated. Thanks. Nisha P -- 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 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] Ions and charge groups
Hi, thanks for the very fast reply. I used pdb2gmx just to build the protein. Then i wrote my own topology including the itp file for the protein and for the atp molecule. I added the ions then. From a pdb file I solvated proteon(6 proteins)+atp+ions and added the water to the top file, that came to look something like [ system ] ; Name system in water [ molecules ] ; Compound #mols protein6 atp 1 CL 48 K 16 SOL 53231 This way, I get that weird behavior about bonds for CL atoms. Doing a couple of further tests I actually solved the problem inverting water and ions both in coordinates and topology, i.e. [ molecules ] ; Compound #mols protein6 atp 1 SOL 53231 CL 48 K 16 Everything now is fine, I successfully minimized and running a short simulation doesn't complain about anything. I think is a pretty strange behavior and I don't understand why I'm forced to put ions after water. Looks like a little bug to me, but I'm not expert enough to be sure. Anyway, thank you a lot for your help. Guido Guido Polles wrote: Hi everybody, Sorry about this, but I'm pretty new to gromacs and I couldn't find any clue about my problem in the archives or in the manual. I'm using gromacs 4.5.1, and my system is a rather big system (about 12x12x12) that includes a proteon, an atp molecule, water and some ions. I am using ffamber99sb force field. Now, I post the log for my mdrun. Initializing Domain Decomposition on 2 nodes Dynamic load balancing: auto Will sort the charge groups at every domain (re)decomposition Initial maximum inter charge-group distances: two-body bonded interactions: 14.813 nm, LJ-14, atoms 25682 25685 multi-body bonded interactions: 14.813 nm, Angle, atoms 25685 25686 Minimum cell size due to bonded interactions: 16.294 nm Using 0 separate PME nodes Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25 Optimizing the DD grid for 2 cells with a minimum initial size of 20.368 nm The maximum allowed number of cells is: X 0 Y 0 Z 0 --- Program mdrun, VERSION 4.5.1 Source code file: domdec.c, line: 6428 Fatal error: There is no domain decomposition for 2 nodes that is compatible with the given box and a minimum cell size of 20.368 nm Change the number of nodes or mdrun option -rdd or -dds Look in the log file for details on the domain decomposition For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Of course the main point here is this Initial maximum inter charge-group distances: two-body bonded interactions: 14.813 nm, LJ-14, atoms 25682 25685 multi-body bonded interactions: 14.813 nm, Angle, atoms 25685 25686 but they're CL ions! Why should they have any bonded interaction or angle interaction?? They shouldn't. Check your [bonds] and [angles] directives for these atom numbers. Apparently mdrun is finding bonds to these ions in your topology. Were these ions added with genion? Present in the initial structure processed by pdb2gmx? Manually added in some location? Actually, I made some tests, and: 1- if I solvate the protein+atp+ions (I want the ions to be in specific positions) system I get that 14nm bond error when I run mdrun, but grompp let it go. OK, so you want ions in specific positions. Did you put them there? If so, was it before or after you generated the topology (presumably with pdb2gmx)? 2- in this situation, if I move in the gro file the coords for the ions after the water, same happens but now grompp throws a warning about charge group distance. That's probably related to the contents of your .mdp file, which you haven't posted. It may or may not be related to the problem at hand. 3- if I solvate then use genion to include the ions at least the simulation starts. Then I get this error A charge group moved too far between two domain decomposition steps, but that is probably related to my system That error message indicates your system has become unstable, likely due to insufficient energy minimization or equilibration, or incorrect .mdp settings. http://www.gromacs.org/Documentation/Terminology/Blowing_Up -Justin I really don't get what's going on here. Thank you in advance for any feedback. Guido -- 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 -- Message: 3 Date: Tue, 30 Nov 2010 14:10:05 -0500 From: Justin A. Lemkul jalem...@vt.edu Subject: Re:
Re: [gmx-users] Ions and charge groups
Guido Polles wrote: Hi, thanks for the very fast reply. I used pdb2gmx just to build the protein. Then i wrote my own topology including the itp file for the protein and for the atp molecule. I added the ions then. From a pdb file I solvated proteon(6 proteins)+atp+ions and added the water to the top file, that came to look something like [ system ] ; Name system in water [ molecules ] ; Compound #mols protein6 atp 1 CL 48 K 16 SOL 53231 This way, I get that weird behavior about bonds for CL atoms. Doing a couple of further tests I actually solved the problem inverting water and ions both in coordinates and topology, i.e. [ molecules ] ; Compound #mols protein6 atp 1 SOL 53231 CL 48 K 16 Everything now is fine, I successfully minimized and running a short simulation doesn't complain about anything. I think is a pretty strange behavior and I don't understand why I'm forced to put ions after water. Looks like a little bug to me, but I'm not expert enough to be sure. Did you get any warnings from grompp that the names in the coordinate file and topology did not match? My guess is yes. The [molecules] directive must match the order of the coordinate file, otherwise the wrong parameters are applied to the wrong species. If this is the case, the bonds involving CL were a result of SOL (water) bonded parameters being applied to CL atoms. -Justin Anyway, thank you a lot for your help. Guido Guido Polles wrote: Hi everybody, Sorry about this, but I'm pretty new to gromacs and I couldn't find any clue about my problem in the archives or in the manual. I'm using gromacs 4.5.1, and my system is a rather big system (about 12x12x12) that includes a proteon, an atp molecule, water and some ions. I am using ffamber99sb force field. Now, I post the log for my mdrun. Initializing Domain Decomposition on 2 nodes Dynamic load balancing: auto Will sort the charge groups at every domain (re)decomposition Initial maximum inter charge-group distances: two-body bonded interactions: 14.813 nm, LJ-14, atoms 25682 25685 multi-body bonded interactions: 14.813 nm, Angle, atoms 25685 25686 Minimum cell size due to bonded interactions: 16.294 nm Using 0 separate PME nodes Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25 Optimizing the DD grid for 2 cells with a minimum initial size of 20.368 nm The maximum allowed number of cells is: X 0 Y 0 Z 0 --- Program mdrun, VERSION 4.5.1 Source code file: domdec.c, line: 6428 Fatal error: There is no domain decomposition for 2 nodes that is compatible with the given box and a minimum cell size of 20.368 nm Change the number of nodes or mdrun option -rdd or -dds Look in the log file for details on the domain decomposition For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Of course the main point here is this Initial maximum inter charge-group distances: two-body bonded interactions: 14.813 nm, LJ-14, atoms 25682 25685 multi-body bonded interactions: 14.813 nm, Angle, atoms 25685 25686 but they're CL ions! Why should they have any bonded interaction or angle interaction?? They shouldn't. Check your [bonds] and [angles] directives for these atom numbers. Apparently mdrun is finding bonds to these ions in your topology. Were these ions added with genion? Present in the initial structure processed by pdb2gmx? Manually added in some location? Actually, I made some tests, and: 1- if I solvate the protein+atp+ions (I want the ions to be in specific positions) system I get that 14nm bond error when I run mdrun, but grompp let it go. OK, so you want ions in specific positions. Did you put them there? If so, was it before or after you generated the topology (presumably with pdb2gmx)? 2- in this situation, if I move in the gro file the coords for the ions after the water, same happens but now grompp throws a warning about charge group distance. That's probably related to the contents of your .mdp file, which you haven't posted. It may or may not be related to the problem at hand. 3- if I solvate then use genion to include the ions at least the simulation starts. Then I get this error A charge group moved too far between two domain decomposition steps, but that is probably related to my system That error message indicates your system has become unstable, likely due to insufficient energy minimization or equilibration, or incorrect .mdp settings. http://www.gromacs.org/Documentation/Terminology/Blowing_Up -Justin I really don't get what's going on here. Thank you in advance for any feedback. Guido -- Justin A. Lemkul Ph.D.
Re: [gmx-users] Ions and charge groups
Oh my, you're totally right. I was ignoring that because I had a coordinate file with hydrogen names from amber, and checking my coordinate file I realized the atp was after the ions. How embarrassing. Sorry for wasting your time. Thank you again Guido 2010/12/1 Justin A. Lemkul jalem...@vt.edu: Guido Polles wrote: Hi, thanks for the very fast reply. I used pdb2gmx just to build the protein. Then i wrote my own topology including the itp file for the protein and for the atp molecule. I added the ions then. From a pdb file I solvated proteon(6 proteins)+atp+ions and added the water to the top file, that came to look something like [ system ] ; Name system in water [ molecules ] ; Compound #mols protein 6 atp 1 CL 48 K 16 SOL 53231 This way, I get that weird behavior about bonds for CL atoms. Doing a couple of further tests I actually solved the problem inverting water and ions both in coordinates and topology, i.e. [ molecules ] ; Compound #mols protein 6 atp 1 SOL 53231 CL 48 K 16 Everything now is fine, I successfully minimized and running a short simulation doesn't complain about anything. I think is a pretty strange behavior and I don't understand why I'm forced to put ions after water. Looks like a little bug to me, but I'm not expert enough to be sure. Did you get any warnings from grompp that the names in the coordinate file and topology did not match? My guess is yes. The [molecules] directive must match the order of the coordinate file, otherwise the wrong parameters are applied to the wrong species. If this is the case, the bonds involving CL were a result of SOL (water) bonded parameters being applied to CL atoms. -Justin Anyway, thank you a lot for your help. Guido Guido Polles wrote: Hi everybody, Sorry about this, but I'm pretty new to gromacs and I couldn't find any clue about my problem in the archives or in the manual. I'm using gromacs 4.5.1, and my system is a rather big system (about 12x12x12) that includes a proteon, an atp molecule, water and some ions. I am using ffamber99sb force field. Now, I post the log for my mdrun. Initializing Domain Decomposition on 2 nodes Dynamic load balancing: auto Will sort the charge groups at every domain (re)decomposition Initial maximum inter charge-group distances: two-body bonded interactions: 14.813 nm, LJ-14, atoms 25682 25685 multi-body bonded interactions: 14.813 nm, Angle, atoms 25685 25686 Minimum cell size due to bonded interactions: 16.294 nm Using 0 separate PME nodes Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25 Optimizing the DD grid for 2 cells with a minimum initial size of 20.368 nm The maximum allowed number of cells is: X 0 Y 0 Z 0 --- Program mdrun, VERSION 4.5.1 Source code file: domdec.c, line: 6428 Fatal error: There is no domain decomposition for 2 nodes that is compatible with the given box and a minimum cell size of 20.368 nm Change the number of nodes or mdrun option -rdd or -dds Look in the log file for details on the domain decomposition For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Of course the main point here is this Initial maximum inter charge-group distances: two-body bonded interactions: 14.813 nm, LJ-14, atoms 25682 25685 multi-body bonded interactions: 14.813 nm, Angle, atoms 25685 25686 but they're CL ions! Why should they have any bonded interaction or angle interaction?? They shouldn't. Check your [bonds] and [angles] directives for these atom numbers. Apparently mdrun is finding bonds to these ions in your topology. Were these ions added with genion? Present in the initial structure processed by pdb2gmx? Manually added in some location? Actually, I made some tests, and: 1- if I solvate the protein+atp+ions (I want the ions to be in specific positions) system I get that 14nm bond error when I run mdrun, but grompp let it go. OK, so you want ions in specific positions. Did you put them there? If so, was it before or after you generated the topology (presumably with pdb2gmx)? 2- in this situation, if I move in the gro file the coords for the ions after the water, same happens but now grompp throws a warning about charge group distance. That's probably related to the contents of your .mdp file, which you haven't posted. It may or may not be related to the problem at hand. 3- if I solvate then use genion to include the ions at least the simulation starts. Then I get this error A charge group moved too far between two domain decomposition steps, but that is probably related to my system That error
Re: [gmx-users] changing the velocity in trajectory file
dear all, can anybody tell me what happens to the velocity of intial config when i use the stochastic integrator like bd or sd. reagrds, sree. On Tue, Nov 30, 2010 at 11:11 AM, Lutz Maibaum lutz.maib...@gmail.comwrote: On Nov 29, 2010, at 8:52 PM, sreelakshmi ramesh wrote: Lutz ya you are true but as you said how can i change the velocity for a config every move as in TPS?since i have not done tps i have no idea abt this. You can't, neither for TPS nor for FFS. I don't think Gromacs provides this functionality. You will have to write your own code that reads positions and velocities from a trajectory file, modifies the velocities, and writes positions and velocities to a file that Gromacs can use as an initial configuration. Alternatively, you can use a stochastic integrator (like Brownian dynamics) and set ld_seed to -1. This way, even identical initial configurations will result in different trajectories. -- Lutz -- 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] water-air interface
Hi everyone, I first created 3 x 3 x 3 nm water, 895 water using genbox. Then i used editconf -bt triclinic -f tension.gro -o conf.gro -c -box 3 3 9 -angles 90 90 90 make the water in x=y=3, z=9 nm box. Then grompp -f em.mdp -c conf.gro -p topol.top -o em.tpr -po mdout2.mdp -maxwarn 10 mdrun -v -s em -e pr -o pr -c after_pr Steepest Descents: Tolerance (Fmax) = 5.0e+01 Number of steps = 10 Step= 0, Dmax= 1.0e-02 nm, Epot= -2.26219e+04 Fmax= 1.42837e+04, atom= 379 Step= 1, Dmax= 1.0e-02 nm, Epot= -2.54567e+04 Fmax= 5.60900e+03, atom= 1870 Step= 2, Dmax= 1.2e-02 nm, Epot= -2.83385e+04 Fmax= 2.94370e+03, atom= 283 Step= 3, Dmax= 1.4e-02 nm, Epot= -3.05598e+04 Fmax= 1.45800e+03, atom= 2077 Step= 4, Dmax= 1.7e-02 nm, Epot= -3.28940e+04 Fmax= 9.07848e+02, atom= 1726 Step= 5, Dmax= 2.1e-02 nm, Epot= -3.49312e+04 Fmax= 1.90443e+03, atom= 1726 Step= 6, Dmax= 2.5e-02 nm, Epot= -3.55885e+04 Fmax= 1.64255e+03, atom= 1726 Step= 7, Dmax= 3.0e-02 nm, Epot= -3.62927e+04 Fmax= 1.83479e+03, atom= 1726 Step= 8, Dmax= 3.6e-02 nm, Epot= -3.68613e+04 Fmax= 2.20746e+03, atom= 1726 Step= 9, Dmax= 4.3e-02 nm, Epot= -3.73153e+04 Fmax= 2.09106e+03, atom= 1726 t = 0.010 ps: Water molecule starting at atom 1726 can not be settled. Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates Step= 10, Dmax= 5.2e-02 nm, Epot= -3.77143e+04 Fmax= 7.92103e+04, atom= 1727 Step= 26, Dmax= 1.9e-06 nm, Epot= -3.25046e+04 Fmax= 2.08556e+05, atom= 1930 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 50 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) writing lowest energy coordinates. Steepest Descents converged to machine precision in 27 steps, but did not reach the requested Fmax 50. Potential Energy = -3.7714320e+04 Maximum force = 7.9210281e+04 on atom 1727 Norm of force = 2.0394656e+03 grompp -f grompp.mdp -c after_pr.gro -p topol.top -o run.tpr -po mdout3.mdp -maxwarn 10 uqtpe...@ce102-0419:~/water/surfacetension/339$ mdrun -v -s run -e pr2 -o pr2 -c after_pr2 -g prlog pr.job Program mdrun, VERSION 4.0.7 Source code file: ../../../../src/mdlib/nsgrid.c, line: 348 Fatal error: Number of grid cells is zero. Probably the system and box collapsed. So my problem is whether my EM result is good? and why the Number of grid cells is zero?? Thanks -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] add a new force field to the pdb2gmx list
Dear all, I have constructed a new CG force field named polycg, and added them to direction ..$GMXLIB/polycg.ff. Can anybody tell me how to add my new force field to gromacs default force field list, in case I can use it to convert pdb files in program pdb2gmx. My gromacs version is 4.5. There is not FF.dat file in direction $GMXLIB any more. I will be very appreciate for your help. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] add a new force field to the pdb2gmx list
Please use find to locate FF.dat in your particular installation. Regards, Yang Ye On Wed, Dec 1, 2010 at 12:17 PM, Jia Haitao jiahai...@gmail.com wrote: Dear all, I have constructed a new CG force field named polycg, and added them to direction ..$GMXLIB/polycg.ff. Can anybody tell me how to add my new force field to gromacs default force field list, in case I can use it to convert pdb files in program pdb2gmx. My gromacs version is 4.5. There is not FF.dat file in direction $GMXLIB any more. I will be very appreciate for your help. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] add a new force field to the pdb2gmx list
On 1/12/2010 3:17 PM, Jia Haitao wrote: Dear all, I have constructed a new CG force field named polycg, and added them to direction ..$GMXLIB/polycg.ff. Can anybody tell me how to add my new force field to gromacs default force field list, in case I can use it to convert pdb files in program pdb2gmx. My gromacs version is 4.5. There is not FF.dat file in direction $GMXLIB any more. I will be very appreciate for your help. Look at the contents for the other force fields. There's probably something you don't have, like forcefield.doc Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] add a new force field to the pdb2gmx list
On 1/12/2010 3:20 PM, Yang Ye wrote: Please use find to locate FF.dat in your particular installation. That mechanism is deprecated in GROMACS 4.5, like the OP said :-) Mark Regards, Yang Ye On Wed, Dec 1, 2010 at 12:17 PM, Jia Haitao jiahai...@gmail.com mailto:jiahai...@gmail.com wrote: Dear all, I have constructed a new CG force field named polycg, and added them to direction ..$GMXLIB/polycg.ff. Can anybody tell me how to add my new force field to gromacs default force field list, in case I can use it to convert pdb files in program pdb2gmx. My gromacs version is 4.5. There is not FF.dat file in direction $GMXLIB any more. I will be very appreciate for your help. -- gmx-users mailing list gmx-users@gromacs.org mailto: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 mailto: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] water-air interface
On 1/12/2010 2:29 PM, 铁锋 彭 wrote: Hi everyone, I first created 3 x 3 x 3 nm water, 895 water using genbox. Then i used editconf -bt triclinic -f tension.gro -o conf.gro -c -box 3 3 9 -angles 90 90 90 make the water in x=y=3, z=9 nm box. Then grompp -f em.mdp -c conf.gro -p topol.top -o em.tpr -po mdout2.mdp -maxwarn 10 mdrun -v -s em -e pr -o pr -c after_pr Steepest Descents: Tolerance (Fmax) = 5.0e+01 Number of steps= 10 Step=0, Dmax= 1.0e-02 nm, Epot= -2.26219e+04 Fmax= 1.42837e+04, atom= 379 Step=1, Dmax= 1.0e-02 nm, Epot= -2.54567e+04 Fmax= 5.60900e+03, atom= 1870 Step=2, Dmax= 1.2e-02 nm, Epot= -2.83385e+04 Fmax= 2.94370e+03, atom= 283 Step=3, Dmax= 1.4e-02 nm, Epot= -3.05598e+04 Fmax= 1.45800e+03, atom= 2077 Step=4, Dmax= 1.7e-02 nm, Epot= -3.28940e+04 Fmax= 9.07848e+02, atom= 1726 Step=5, Dmax= 2.1e-02 nm, Epot= -3.49312e+04 Fmax= 1.90443e+03, atom= 1726 Step=6, Dmax= 2.5e-02 nm, Epot= -3.55885e+04 Fmax= 1.64255e+03, atom= 1726 Step=7, Dmax= 3.0e-02 nm, Epot= -3.62927e+04 Fmax= 1.83479e+03, atom= 1726 Step=8, Dmax= 3.6e-02 nm, Epot= -3.68613e+04 Fmax= 2.20746e+03, atom= 1726 Step=9, Dmax= 4.3e-02 nm, Epot= -3.73153e+04 Fmax= 2.09106e+03, atom= 1726 t = 0.010 ps: Water molecule starting at atom 1726 can not be settled. Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates Step= 10, Dmax= 5.2e-02 nm, Epot= -3.77143e+04 Fmax= 7.92103e+04, atom= 1727 Step= 26, Dmax= 1.9e-06 nm, Epot= -3.25046e+04 Fmax= 2.08556e+05, atom= 1930 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 50 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) writing lowest energy coordinates. Steepest Descents converged to machine precision in 27 steps, but did not reach the requested Fmax 50. Potential Energy = -3.7714320e+04 Maximum force = 7.9210281e+04 on atom 1727 Norm of force = 2.0394656e+03 grompp -f grompp.mdp -c after_pr.gro -p topol.top -o run.tpr -po mdout3.mdp -maxwarn 10 uqtpe...@ce102-0419:~/water/surfacetension/339$ mdrun -v -s run -e pr2 -o pr2 -c after_pr2 -g prlog pr.job Program mdrun, VERSION 4.0.7 Source code file: ../../../../src/mdlib/nsgrid.c, line: 348 Fatal error: Number of grid cells is zero. Probably the system and box collapsed. So my problem is whether my EM result is good? No, it isn't. There's at least one bad water molecule, like the output said. and why the Number of grid cells is zero?? Because the system imploded. 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] add a new force field to the pdb2gmx list
No, I did not miss any files in direction .ff. I even add a ffpolycg.itp in ../$GMXLIB. Is there any file like FF.dat ? 2010/12/1 Mark Abraham mark.abra...@anu.edu.au On 1/12/2010 3:17 PM, Jia Haitao wrote: Dear all, I have constructed a new CG force field named polycg, and added them to direction ..$GMXLIB/polycg.ff. Can anybody tell me how to add my new force field to gromacs default force field list, in case I can use it to convert pdb files in program pdb2gmx. My gromacs version is 4.5. There is not FF.dat file in direction $GMXLIB any more. I will be very appreciate for your help. Look at the contents for the other force fields. There's probably something you don't have, like forcefield.doc Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] add a new force field to the pdb2gmx list
On 1/12/2010 3:55 PM, Jia Haitao wrote: No, I did not miss any files in direction .ff. I even add a ffpolycg.itp in ../$GMXLIB. Is there any file like FF.dat ? See pdb2gmx -h Mark 2010/12/1 Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au On 1/12/2010 3:17 PM, Jia Haitao wrote: Dear all, I have constructed a new CG force field named polycg, and added them to direction ..$GMXLIB/polycg.ff. Can anybody tell me how to add my new force field to gromacs default force field list, in case I can use it to convert pdb files in program pdb2gmx. My gromacs version is 4.5. There is not FF.dat file in direction $GMXLIB any more. I will be very appreciate for your help. Look at the contents for the other force fields. There's probably something you don't have, like forcefield.doc Mark -- gmx-users mailing list gmx-users@gromacs.org mailto: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 mailto: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] Reg:Uncertainty in the average value
Hi all I calculated the surface tension of dce (dichloroethane) using the g_energy command and found the average surface tension value to be 30.68 mN/m. what i want to know is how to find the standard error or the uncertainty of the average value in gromacs? i know one should always report the value as 30.68 plus(r)minus ? mN/m. any help is highly appreciated. Regards Vinoth -- 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
