[gmx-users] FATAL ERROR: Residue "LIG" not found in residue topology database.
Dear All usres: I am trying to do a simple system that contains 4 molecules ethane and MD run using GROMACS. I build my .pdb file by using Avogadro software . Afterwards, I try to generate the topology and .gro file using pdb2gmx program and it generates an error. I am using the 43a1 force field. COMPNDUNNAMED AUTHORGENERATED BY OPEN BABEL 2.3.0 HETATM1 C LIG 1 -1.328 5.677 -0.487 1.00 0.00 C HETATM2 C LIG 1 0.160 5.696 -0.216 1.00 0.00 C HETATM3 C LIG 2 -2.612 1.541 -0.437 1.00 0.00 C HETATM4 C LIG 2 -1.247 1.959 0.060 1.00 0.00 C HETATM5 C LIG 3 -0.924 -2.018 0.494 1.00 0.00 C HETATM6 C LIG 3 0.583 -1.901 0.467 1.00 0.00 C HETATM7 C LIG 4 0.836 -5.626 -0.170 1.00 0.00 C HETATM8 C LIG 4 2.339 -5.464 -0.149 1.00 0.00 C HETATM9 H LIG 1 -1.676 6.669 -0.790 1.00 0.00 H HETATM 10 H LIG 1 -1.878 5.379 0.410 1.00 0.00 H HETATM 11 H LIG 1 -1.564 4.970 -1.287 1.00 0.00 H HETATM 12 H LIG 1 0.396 6.406 0.582 1.00 0.00 H HETATM 13 H LIG 1 0.710 5.990 -1.115 1.00 0.00 H HETATM 14 H LIG 1 0.508 4.705 0.091 1.00 0.00 H HETATM 15 H LIG 2 -3.153 2.402 -0.840 1.00 0.00 H HETATM 16 H LIG 2 -3.203 1.113 0.378 1.00 0.00 H HETATM 17 H LIG 2 -2.520 0.790 -1.227 1.00 0.00 H HETATM 18 H LIG 2 -0.651 2.374 -0.758 1.00 0.00 H HETATM 19 H LIG 2 -0.709 1.102 0.476 1.00 0.00 H HETATM 20 H LIG 2 -1.338 2.717 0.843 1.00 0.00 H HETATM 21 H LIG 3 -1.230 -3.068 0.452 1.00 0.00 H HETATM 22 H LIG 3 -1.365 -1.498 -0.362 1.00 0.00 H HETATM 23 H LIG 3 -1.328 -1.578 1.410 1.00 0.00 H HETATM 24 H LIG 3 0.891 -0.853 0.527 1.00 0.00 H HETATM 25 H LIG 3 0.984 -2.323 -0.459 1.00 0.00 H HETATM 26 H LIG 3 1.025 -2.438 1.312 1.00 0.00 H HETATM 27 H LIG 4 2.612 -4.409 -0.060 1.00 0.00 H HETATM 28 H LIG 4 2.771 -6.003 0.699 1.00 0.00 H HETATM 29 H LIG 4 2.781 -5.858 -1.069 1.00 0.00 H HETATM 30 H LIG 4 0.564 -6.681 -0.264 1.00 0.00 H HETATM 31 H LIG 4 0.394 -5.238 0.753 1.00 0.00 H HETATM 32 H LIG 4 0.402 -5.082 -1.015 1.00 0.00 H END FATAL ERROR: Residue "LIG" not found in residue topology database. Sincerely -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] FATAL ERROR: Residue "LIG" not found in residue topology database.
On 7/31/12 7:48 AM, Ali Alizadeh wrote: Dear All usres: I am trying to do a simple system that contains 4 molecules ethane and MD run using GROMACS. I build my .pdb file by using Avogadro software . Afterwards, I try to generate the topology and .gro file using pdb2gmx program and it generates an error. I am using the 43a1 force field. pdb2gmx isn't magic: http://www.gromacs.org/Documentation/Errors#Residue_'XXX'_not_found_in_residue_topology_database -Justin COMPNDUNNAMED AUTHORGENERATED BY OPEN BABEL 2.3.0 HETATM1 C LIG 1 -1.328 5.677 -0.487 1.00 0.00 C HETATM2 C LIG 1 0.160 5.696 -0.216 1.00 0.00 C HETATM3 C LIG 2 -2.612 1.541 -0.437 1.00 0.00 C HETATM4 C LIG 2 -1.247 1.959 0.060 1.00 0.00 C HETATM5 C LIG 3 -0.924 -2.018 0.494 1.00 0.00 C HETATM6 C LIG 3 0.583 -1.901 0.467 1.00 0.00 C HETATM7 C LIG 4 0.836 -5.626 -0.170 1.00 0.00 C HETATM8 C LIG 4 2.339 -5.464 -0.149 1.00 0.00 C HETATM9 H LIG 1 -1.676 6.669 -0.790 1.00 0.00 H HETATM 10 H LIG 1 -1.878 5.379 0.410 1.00 0.00 H HETATM 11 H LIG 1 -1.564 4.970 -1.287 1.00 0.00 H HETATM 12 H LIG 1 0.396 6.406 0.582 1.00 0.00 H HETATM 13 H LIG 1 0.710 5.990 -1.115 1.00 0.00 H HETATM 14 H LIG 1 0.508 4.705 0.091 1.00 0.00 H HETATM 15 H LIG 2 -3.153 2.402 -0.840 1.00 0.00 H HETATM 16 H LIG 2 -3.203 1.113 0.378 1.00 0.00 H HETATM 17 H LIG 2 -2.520 0.790 -1.227 1.00 0.00 H HETATM 18 H LIG 2 -0.651 2.374 -0.758 1.00 0.00 H HETATM 19 H LIG 2 -0.709 1.102 0.476 1.00 0.00 H HETATM 20 H LIG 2 -1.338 2.717 0.843 1.00 0.00 H HETATM 21 H LIG 3 -1.230 -3.068 0.452 1.00 0.00 H HETATM 22 H LIG 3 -1.365 -1.498 -0.362 1.00 0.00 H HETATM 23 H LIG 3 -1.328 -1.578 1.410 1.00 0.00 H HETATM 24 H LIG 3 0.891 -0.853 0.527 1.00 0.00 H HETATM 25 H LIG 3 0.984 -2.323 -0.459 1.00 0.00 H HETATM 26 H LIG 3 1.025 -2.438 1.312 1.00 0.00 H HETATM 27 H LIG 4 2.612 -4.409 -0.060 1.00 0.00 H HETATM 28 H LIG 4 2.771 -6.003 0.699 1.00 0.00 H HETATM 29 H LIG 4 2.781 -5.858 -1.069 1.00 0.00 H HETATM 30 H LIG 4 0.564 -6.681 -0.264 1.00 0.00 H HETATM 31 H LIG 4 0.394 -5.238 0.753 1.00 0.00 H HETATM 32 H LIG 4 0.402 -5.082 -1.015 1.00 0.00 H END FATAL ERROR: Residue "LIG" not found in residue topology database. Sincerely -- Justin A. Lemkul, Ph.D. Research Scientist 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 * Only plain text messages are allowed! * 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] FATAL ERROR Residue "LIG" not found in residue topology database?
Dear All usres: I am trying to do a simple system that contains 4 molecules ethane and MD run using GROMACS. I build my .pdb file by using Avogadro software . Afterwards, I try to generate the topology and .gro file using pdb2gmx program and it generates an error. I am using the 43a1 force field. COMPNDUNNAMED AUTHORGENERATED BY OPEN BABEL 2.3.0 HETATM1 C LIG 1 -1.328 5.677 -0.487 1.00 0.00 C HETATM2 C LIG 1 0.160 5.696 -0.216 1.00 0.00 C HETATM3 C LIG 2 -2.612 1.541 -0.437 1.00 0.00 C HETATM4 C LIG 2 -1.247 1.959 0.060 1.00 0.00 C HETATM5 C LIG 3 -0.924 -2.018 0.494 1.00 0.00 C HETATM6 C LIG 3 0.583 -1.901 0.467 1.00 0.00 C HETATM7 C LIG 4 0.836 -5.626 -0.170 1.00 0.00 C HETATM8 C LIG 4 2.339 -5.464 -0.149 1.00 0.00 C HETATM9 H LIG 1 -1.676 6.669 -0.790 1.00 0.00 H HETATM 10 H LIG 1 -1.878 5.379 0.410 1.00 0.00 H HETATM 11 H LIG 1 -1.564 4.970 -1.287 1.00 0.00 H HETATM 12 H LIG 1 0.396 6.406 0.582 1.00 0.00 H HETATM 13 H LIG 1 0.710 5.990 -1.115 1.00 0.00 H HETATM 14 H LIG 1 0.508 4.705 0.091 1.00 0.00 H HETATM 15 H LIG 2 -3.153 2.402 -0.840 1.00 0.00 H HETATM 16 H LIG 2 -3.203 1.113 0.378 1.00 0.00 H HETATM 17 H LIG 2 -2.520 0.790 -1.227 1.00 0.00 H HETATM 18 H LIG 2 -0.651 2.374 -0.758 1.00 0.00 H HETATM 19 H LIG 2 -0.709 1.102 0.476 1.00 0.00 H HETATM 20 H LIG 2 -1.338 2.717 0.843 1.00 0.00 H HETATM 21 H LIG 3 -1.230 -3.068 0.452 1.00 0.00 H HETATM 22 H LIG 3 -1.365 -1.498 -0.362 1.00 0.00 H HETATM 23 H LIG 3 -1.328 -1.578 1.410 1.00 0.00 H HETATM 24 H LIG 3 0.891 -0.853 0.527 1.00 0.00 H HETATM 25 H LIG 3 0.984 -2.323 -0.459 1.00 0.00 H HETATM 26 H LIG 3 1.025 -2.438 1.312 1.00 0.00 H HETATM 27 H LIG 4 2.612 -4.409 -0.060 1.00 0.00 H HETATM 28 H LIG 4 2.771 -6.003 0.699 1.00 0.00 H HETATM 29 H LIG 4 2.781 -5.858 -1.069 1.00 0.00 H HETATM 30 H LIG 4 0.564 -6.681 -0.264 1.00 0.00 H HETATM 31 H LIG 4 0.394 -5.238 0.753 1.00 0.00 H HETATM 32 H LIG 4 0.402 -5.082 -1.015 1.00 0.00 H END FATAL ERROR: Residue "LIG" not found in residue topology database. Sincerely -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] make_ndx: duplicates groups appearing in index.ndx file
Hello, I've just switched from using Gromacs version 4.0.5 to 4.5.5, and I'm having an issue with make_ndx. Using the old version I have a single group showing up for each "odd" residue, eg JJJ shows up once as group 16 for example. When I use the new version on the same file I get 2 groups appearing for residue JJJ and others. Here is the output of that I get from make_ndx. Is there some way I can prevent this? 0 System : 126928 atoms 1 Other : 137 atoms 2 NGL : 9 atoms 3 CY1 :10 atoms 4 CAR :25 atoms 5 HEM :73 atoms 6 JJJ : 1 atoms 7 CPZ :19 atoms 8 Cl : 6 atoms 9 Protein : 7475 atoms 10 Protein-H : 3733 atoms 11 C-alpha : 461 atoms 12 Backbone: 1383 atoms 13 MainChain : 1844 atoms 14 MainChain+Cb: 2275 atoms 15 MainChain+H : 2275 atoms 16 SideChain : 5200 atoms 17 SideChain-H : 1889 atoms 18 Prot-Masses : 7475 atoms 19 non-Protein : 119453 atoms 20 Water : 119310 atoms 21 SOL : 119310 atoms 22 non-Water : 7618 atoms 23 Ion : 6 atoms 24 NGL : 9 atoms 25 CY1 :10 atoms 26 CAR :25 atoms 27 HEM :73 atoms 28 JJJ : 1 atoms 29 CPZ :19 atoms 30 Cl : 6 atoms 31 Water_and_ions : 119316 atoms Thanks, - Laura -- Laura Kingsley Graduate Student Medicinal Chemistry and Molecular Pharmacology Purdue University Office: RHPH 504A 575 Stadium Mall Dr. West Lafayette, IN 47907 Office Phone: (765) 496-6643 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] make_ndx: duplicates groups appearing in index.ndx file
On 7/31/12 10:14 AM, Laura Kingsley wrote: Hello, I've just switched from using Gromacs version 4.0.5 to 4.5.5, and I'm having an issue with make_ndx. Using the old version I have a single group showing up for each "odd" residue, eg JJJ shows up once as group 16 for example. When I use the new version on the same file I get 2 groups appearing for residue JJJ and others. Here is the output of that I get from make_ndx. Is there some way I can prevent this? Repeated groups are normal, but certainly undesirable. Since there is nothing functionally wrong with these groups, it's a rather low-priority bug and has been around since Gromacs 4.5 (so several years). The only way to prevent the duplicate groups would be to create an index file that eliminates the duplicates. -Justin 0 System : 126928 atoms 1 Other : 137 atoms 2 NGL : 9 atoms 3 CY1 :10 atoms 4 CAR :25 atoms 5 HEM :73 atoms 6 JJJ : 1 atoms 7 CPZ :19 atoms 8 Cl : 6 atoms 9 Protein : 7475 atoms 10 Protein-H : 3733 atoms 11 C-alpha : 461 atoms 12 Backbone: 1383 atoms 13 MainChain : 1844 atoms 14 MainChain+Cb: 2275 atoms 15 MainChain+H : 2275 atoms 16 SideChain : 5200 atoms 17 SideChain-H : 1889 atoms 18 Prot-Masses : 7475 atoms 19 non-Protein : 119453 atoms 20 Water : 119310 atoms 21 SOL : 119310 atoms 22 non-Water : 7618 atoms 23 Ion : 6 atoms 24 NGL : 9 atoms 25 CY1 :10 atoms 26 CAR :25 atoms 27 HEM :73 atoms 28 JJJ : 1 atoms 29 CPZ :19 atoms 30 Cl : 6 atoms 31 Water_and_ions : 119316 atoms Thanks, - Laura -- Justin A. Lemkul, Ph.D. Research Scientist 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 * Only plain text messages are allowed! * 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] Isothermal compressibility for polymers - regd
Dear GMX users, How one can calculate Isothermal compressibility for given system ( eg : Materials like polymers ) using gromacs. Thank you in advance. Regards, Ramesh Cheerla. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] Double X Simple precision
Hi folks! I'm running Gromacs in double precision to minimize my system until 10^-4 kcal/mol.nm 'cause it's too much unstable. Unfortunately, my system is huge and double precision make the simulation slower. My question is: can I run minimization process in double precision and simulation itself in simple?? Thanks! -- Marcelo -- View this message in context: http://gromacs.5086.n6.nabble.com/Double-X-Simple-precision-tp4999894.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: Double X Simple precision
marcelodepolo wrote > > I'm running Gromacs in double precision to minimize my system until 10^-4 > kcal/mol.nm 'cause it's too much unstable. Unfortunately, my system is > huge and double precision make the simulation slower. > > My question is: can I run minimization process in double precision and > simulation itself in simple?? Yes. This may not help your problem. See http://www.gromacs.org/Documentation/Terminology/Blowing_Up Mark -- View this message in context: http://gromacs.5086.n6.nabble.com/Double-X-Simple-precision-tp4999894p4999895.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] Molecule in topology has atom numbers below and above natoms
Hello Everybody I'm running a production simulation of a kinase (after minimization and equilibration) and after concluded 20ns I got the following problem when I tryied to run g_rmsf "Fatal error: Molecule in topology has atom numbers below and above natoms (4005). You are probably trying to use a trajectory which does not match the first 4005 atoms of the run input file. You can make a matching run input file with tpbconv. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors"; I insert ions in the PDB and ATP. My ion's topology were included as: "#include "WT_Other_chain_A2.itp", #include "WT_Other_chain_B2.itp"". I don't know if they're causing the trouble. tks for help -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: Molecule in topology has atom numbers below and above natoms
Thales Kronenberger wrote > > Hello Everybody > > I'm running a production simulation of a kinase (after minimization > and equilibration) and after concluded 20ns I got the following > problem when I tryied to run g_rmsf > > "Fatal error: > Molecule in topology has atom numbers below and above natoms (4005). > You are probably trying to use a trajectory which does not match the > first 4005 atoms of the run input file. > You can make a matching run input file with tpbconv. > For more information and tips for troubleshooting, please check the > GROMACS > website at http://www.gromacs.org/Documentation/Errors"; > > I insert ions in the PDB and ATP. My ion's topology were included as: > "#include "WT_Other_chain_A2.itp", #include "WT_Other_chain_B2.itp"". > I don't know if they're causing the trouble > They aren't. But like the error message says, until you know what the coordinates in your trajectory file represent, and how that relates to the run input file you gave to g_rmsf it will be a mystery. Mark -- View this message in context: http://gromacs.5086.n6.nabble.com/Molecule-in-topology-has-atom-numbers-below-and-above-natoms-tp4999896p4999897.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] Diagnosing + system blowing up
Thanks for dear Mark's suggestions. What's the typical solution to fix such errors of grompp? I don't have any idea to do what, so erased the lines defined in output of grompp, then I went through the NVT equilibrium, it didn't stop by multiple interaction errors. I don't know what will happen for the rest of the investigation, put the protein in bilayer and then Umbrella Sampling and . . If anybody has suggestion, it would be appreciated. Sincerely, Shima From: Shima Arasteh To: Discussion list for GROMACS users Sent: Tuesday, July 31, 2012 4:49 AM Subject: Re: [gmx-users] Diagnosing + system blowing up I edited the grompp output and sent it to you. Bring that again here: Generated 21528 of the 21528 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 18355 of the 21528 1-4 parameter combinations ERROR 1 [file topol.top, line 414]: No default Bond types ERROR 2 [file topol.top, line 1698]: No default U-B types ERROR 3 [file topol.top, line 1699]: No default U-B types ERROR 4 [file topol.top, line 2345]: No default Proper Dih. types ERROR 5 [file topol.top, line 2346]: No default Proper Dih. types ERROR 6 [file topol.top, line 3278]: No default Improper Dih. types And wrote line 414 is : line 414 of topol.tp: [bonds] 1 2 1 Sincerely, Shima From: Mark Abraham To: Discussion list for GROMACS users Sent: Tuesday, July 31, 2012 4:40 AM Subject: Re: [gmx-users] Diagnosing + system blowing up On 31/07/2012 7:16 AM, Shima Arasteh wrote: > Wow! That was a fabulous explanation given to me. Thanks dear Mark! :-) > > I regenerated the topol.top to check the correctness of input and FF files. > Some output has been changed however a little bit. Now, I bring you all was > needed again: > >> 1. rtp entry >> >> [ FVAL ] > [ atoms ] > CN C 0.357 0 > ON O -0.51 1 > H1 HA 0.100 2 > N NH1 -0.423 3 > HN H 0.333 4 > CA CT1 0.034 5 > HA HB 0.09 6 > CB CT1 -0.093 7 > HB HA 0.09 8 > CG1 CT3 -0.268 9 > HG11 HA 0.09 10 > HG12 HA 0.09 11 > HG13 HA 0.09 12 > CG2 CT3 -0.268 13 > HG21 HA 0.09 14 > HG22 HA 0.09 15 > HG23 HA 0.09 16 > C C 0.528 17 > O O -0.510 18 > [ bonds ] > CN H1 > CN ON > CN N > N HN > CA N > CA HA > CA C > C O > CA CB > CB HB > CB CG1 > CB CG2 > CG2 HG21 > CG2 HG22 > CG2 HG23 > CG1 HG11 > CG1 HG12 > CG1 HG13 > > [ impropers ] > CN N ON H1 > >> 2. hdb entry > In which file? > *aminoacids.hdb > > >> FVAL 6 >> 1 1 H1 CN N ON > This should be generating H1 bonded to CN... > >> 1 1 HN N C CA >> 1 5 HA CA N C CB >> 1 5 HB CB CA CG1 CG2 >> 3 4 HG1 CG1 CB CA >> 3 4 HG2 CG2 CB CA >> >> 3. N-terminal fragment >> HETATM 1 CN FVAL 1 -0.721 1.600 1.249 >> HETATM 2 ON FVAL 1 -0.839 2.806 1.453 >> ATOM 3 N FVAL 1 -1.227 0.728 2.125 >> ATOM 4 CA FVAL 1 -1.918 1.159 3.323 >> ATOM 5 C FVAL 1 -1.969 2.678 3.410 >> ATOM 6 O FVAL 1 -0.931 3.335 3.447 >> ATOM 7 CB FVAL 1 -1.219 0.644 4.576 >> ATOM 8 CG1 FVAL 1 0.208 1.178 4.618 >> ATOM 9 CG2 FVAL 1 -1.976 1.118 5.812 >> >> 4. pdb2gmx command >> #pdb2gmx -f monomer.pdb -o monomer.gro -water tip3p -ter >> >> 5. pdb2gmx output > Using the Charmm36-modified force field in directory ./charmm36-modified.ff > > Opening force field file ./charmm36-modified.ff/aminoacids.r2b > Opening force field file ./charmm36-modified.ff/rna.r2b > Reading monomer.pdb... > Read 177 atoms > Analyzing pdb file > Splitting chemical chains based on TER records or chain id changing. > There are 1 chains and 0 blocks of water and 24 residues with 177 atoms > > chain #res #atoms > 1 ' ' 24 177 > > All occupancy fields zero. This is probably not an X-Ray structure > Opening force field file ./charmm36-modified.ff/atomtypes.atp > Atomtype 1 > Reading residue database... (charmm36-modified) > Opening force field file ./charmm36-modified.ff/aminoacids.rtp > Residue 42 > Sorting it all out... > Opening force field file ./charmm36-modified.ff/dna.rtp > Residue 46 > Sorting it all out... > Opening force field file ./charmm36-modified.ff/lipids.rtp > Residue 82 > Sorting it all out... > Opening force field file ./charmm36-modified.ff/rna.rtp > Residue 86 > Sorting it all out... > Opening force field file ./charmm
Re: [gmx-users] Diagnosing + system blowing up
On 7/31/12 5:21 PM, Shima Arasteh wrote: Thanks for dear Mark's suggestions. What's the typical solution to fix such errors of grompp? I don't have any idea to do what, so erased the lines defined in output of grompp, then I went through the NVT equilibrium, it didn't stop by multiple interaction errors. I don't know what will happen for the rest of the investigation, put the protein in bilayer and then Umbrella Sampling and . . If anybody has suggestion, it would be appreciated. You shouldn't delete lines from the topology. The errors indicate that the interaction types you have defined do not exist in the force field. You need to add suitable values, either by analogy to existing parameters or by a suitable derivation protocol. I would not trust any results from a topology that has been haphazardly modified in this way. You may get rid of the grompp warnings, but you also get rid of reliability. -Justin Sincerely, Shima From: Shima Arasteh To: Discussion list for GROMACS users Sent: Tuesday, July 31, 2012 4:49 AM Subject: Re: [gmx-users] Diagnosing + system blowing up I edited the grompp output and sent it to you. Bring that again here: Generated 21528 of the 21528 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 18355 of the 21528 1-4 parameter combinations ERROR 1 [file topol.top, line 414]: No default Bond types ERROR 2 [file topol.top, line 1698]: No default U-B types ERROR 3 [file topol.top, line 1699]: No default U-B types ERROR 4 [file topol.top, line 2345]: No default Proper Dih. types ERROR 5 [file topol.top, line 2346]: No default Proper Dih. types ERROR 6 [file topol.top, line 3278]: No default Improper Dih. types And wrote line 414 is : line 414 of topol.tp: [bonds] 1 2 1 Sincerely, Shima From: Mark Abraham To: Discussion list for GROMACS users Sent: Tuesday, July 31, 2012 4:40 AM Subject: Re: [gmx-users] Diagnosing + system blowing up On 31/07/2012 7:16 AM, Shima Arasteh wrote: Wow! That was a fabulous explanation given to me. Thanks dear Mark! :-) I regenerated the topol.top to check the correctness of input and FF files. Some output has been changed however a little bit. Now, I bring you all was needed again: 1. rtp entry [ FVAL ] [ atoms ] CNC 0.3570 ONO-0.511 H1HA0.1002 NNH1-0.4233 HNH0.3334 CACT10.0345 HAHB0.096 CBCT1-0.0937 HBHA0.098 CG1CT3-0.2689 HG11HA0.0910 HG12HA0.0911 HG13HA0.0912 CG2CT3-0.26813 HG21HA0.0914 HG22HA0.0915 HG23HA0.0916 CC0.52817 OO-0.51018 [ bonds ] CNH1 CNON CNN NHN CAN CAHA CAC CO CACB CBHB CBCG1 CBCG2 CG2HG21 CG2HG22 CG2HG23 CG1HG11 CG1HG12 CG1HG13 [ impropers ] CN NONH1 2. hdb entry In which file? *aminoacids.hdb FVAL6 11H1CNNON This should be generating H1 bonded to CN... 11HNNCCA 15HACANCCB 15HBCBCACG1CG2 34HG1CG1CBCA 34HG2CG2CBCA 3. N-terminal fragment HETATM1 CN FVAL1 -0.721 1.600 1.249 HETATM2 ON FVAL1 -0.839 2.806 1.453 ATOM 3 N FVAL1 -1.227 0.728 2.125 ATOM 4 CA FVAL1 -1.918 1.159 3.323 ATOM 5 C FVAL1 -1.969 2.678 3.410 ATOM 6 O FVAL1 -0.931 3.335 3.447 ATOM 7 CB FVAL1 -1.219 0.644 4.576 ATOM 8 CG1 FVAL1 0.208 1.178 4.618 ATOM 9 CG2 FVAL1 -1.976 1.118 5.812 4. pdb2gmx command #pdb2gmx -f monomer.pdb -o monomer.gro -water tip3p -ter 5. pdb2gmx output Using the Charmm36-modified force field in directory ./charmm36-modified.ff Opening force field file ./charmm36-modified.ff/aminoacids.r2b Opening force field file ./charmm36-modified.ff/rna.r2b Reading monomer.pdb... Read 177 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 24 residues with 177 atoms chain #res #atoms 1 ' '24177 All occupancy fields zero. This is probably not an X-Ray structure Opening force field file ./charmm36-modified.ff/atomtypes.atp Atomtype 1 Reading residue database... (charmm36-modified) Opening force field file ./charmm36-m
Re: [gmx-users] Diagnosing + system blowing up
All right. Thanks. Sincerely, Shima - Original Message - From: Justin Lemkul To: Shima Arasteh ; Discussion list for GROMACS users Cc: Sent: Wednesday, August 1, 2012 2:04 AM Subject: Re: [gmx-users] Diagnosing + system blowing up On 7/31/12 5:21 PM, Shima Arasteh wrote: > Thanks for dear Mark's suggestions. > > What's the typical solution to fix such errors of grompp? > I don't have any idea to do what, so erased the lines defined in output of > grompp, then I went through the NVT equilibrium, it didn't stop by multiple > interaction errors. I don't know what will happen for the rest of the > investigation, put the protein in bilayer and then Umbrella Sampling and > . . > If anybody has suggestion, it would be appreciated. > You shouldn't delete lines from the topology. The errors indicate that the interaction types you have defined do not exist in the force field. You need to add suitable values, either by analogy to existing parameters or by a suitable derivation protocol. I would not trust any results from a topology that has been haphazardly modified in this way. You may get rid of the grompp warnings, but you also get rid of reliability. -Justin > > Sincerely, > Shima > > > > From: Shima Arasteh > To: Discussion list for GROMACS users > Sent: Tuesday, July 31, 2012 4:49 AM > Subject: Re: [gmx-users] Diagnosing + system blowing up > > I edited the grompp output and sent it to you. Bring that again here: > Generated 21528 of the 21528 non-bonded parameter combinations > Generating 1-4 interactions: fudge = 1 > Generated 18355 of the 21528 1-4 parameter combinations > > ERROR 1 [file topol.top, line 414]: > No default Bond types > > > ERROR 2 [file topol.top, line 1698]: > No default U-B types > > > ERROR 3 [file topol.top, line 1699]: > No default U-B types > > > ERROR 4 [file topol.top, line 2345]: > No default Proper Dih. types > > > ERROR 5 [file topol.top, line 2346]: > No default Proper Dih. types > > ERROR 6 [file topol.top, line 3278]: > No default Improper Dih. types > > And wrote line 414 is : > line 414 of topol.tp: > [bonds] > 1 2 1 > > > > Sincerely, > Shima > > > > From: Mark Abraham > To: Discussion list for GROMACS users > Sent: Tuesday, July 31, 2012 4:40 AM > Subject: Re: [gmx-users] Diagnosing + system blowing up > > On 31/07/2012 7:16 AM, Shima Arasteh wrote: >> Wow! That was a fabulous explanation given to me. Thanks dear Mark! :-) >> >> I regenerated the topol.top to check the correctness of input and FF files. >> Some output has been changed however a little bit. Now, I bring you all was >> needed again: >> >>> 1. rtp entry >>> >>> [ FVAL ] >> [ atoms ] >> CN C 0.357 0 >> ON O -0.51 1 >> H1 HA 0.100 2 >> N NH1 -0.423 3 >> HN H 0.333 4 >> CA CT1 0.034 5 >> HA HB 0.09 6 >> CB CT1 -0.093 7 >> HB HA 0.09 8 >> CG1 CT3 -0.268 9 >> HG11 HA 0.09 10 >> HG12 HA 0.09 11 >> HG13 HA 0.09 12 >> CG2 CT3 -0.268 13 >> HG21 HA 0.09 14 >> HG22 HA 0.09 15 >> HG23 HA 0.09 16 >> C C 0.528 17 >> O O -0.510 18 >> [ bonds ] >> CN H1 >> CN ON >> CN N >> N HN >> CA N >> CA HA >> CA C >> C O >> CA CB >> CB HB >> CB CG1 >> CB CG2 >> CG2 HG21 >> CG2 HG22 >> CG2 HG23 >> CG1 HG11 >> CG1 HG12 >> CG1 HG13 >> >> [ impropers ] >> CN N ON H1 >> >>> 2. hdb entry >> In which file? >> *aminoacids.hdb >> >> >>> FVAL 6 >>> 1 1 H1 CN N ON >> This should be generating H1 bonded to CN... >> >>> 1 1 HN N C CA >>> 1 5 HA CA N C CB >>> 1 5 HB CB CA CG1 CG2 >>> 3 4 HG1 CG1 CB CA >>> 3 4 HG2 CG2 CB CA >>> >>> 3. N-terminal fragment >>> HETATM 1 CN FVAL 1 -0.721 1.600 1.249 >>> HETATM 2 ON FVAL 1 -0.839 2.806 1.453 >>> ATOM 3 N FVAL 1 -1.227 0.728 2.125 >>> ATOM 4 CA FVAL 1 -1.918 1.159 3.323 >>> ATOM 5 C FVAL 1 -1.969 2.678 3.410 >>> ATOM 6 O FVAL 1 -0.931 3.335 3.447 >>> ATOM 7 CB FVAL 1 -1.219 0.644 4.576 >>> ATOM 8 CG1 FVAL 1 0.208 1.178 4.618 >>> ATOM 9 CG2 FVAL 1 -1.976 1.118 5.812 >>> >>> 4. pdb2gmx command >>> #pdb2gmx -f monomer.pdb -o monomer.gro -water tip3p -ter >>> >>> 5. pdb2gmx output >> Using the Charmm36-modified force field in directory ./ch
[gmx-users] Re: Diagnosing + system blowing up
Shima Arasteh wrote > > Thanks for dear Mark's suggestions. > > What's the typical solution to fix such errors of grompp? > As I've said lots of times, you need to go and look at the atom types you're using, what interactions are defined for them in ffbonded.itp and perhaps reassess those types. Perhaps you can invent some interactions by analogy. Perhaps you can parameterise some. Perhaps you should give up and use acetyl. Shima Arasteh wrote > I don't have any idea to do what, so erased the lines defined in output of > grompp, As Justin said, blindly deleting things is a terrible approach. This assumes that pdb2gmx created interactions that weren't useful to your model physics, given the fact that you've forced it to use atom types that the makers didn't intend. It's much more likely you're doing something wrong than pdb2gmx is doing something wrong. Shima Arasteh wrote > then I went through the NVT equilibrium, it didn't stop by multiple > interaction errors. I don't know what will happen for the rest of the > investigation, put the protein in bilayer and then Umbrella Sampling and > . . No point worrying about that yet. You're trying to run a simulation on a species that your force field didn't anticipate. So you've got to fix that, or choose a different force field, or a different simulation. Shima Arasteh wrote > ERROR 1 [file topol.top, line 414]: > No default Bond types > > And wrote line 414 is : > line 414 of topol.tp: > [bonds] > 1 2 1 > Think about this. grompp couldn't find a bonded interaction of type 1 that matched atoms 1 and 2. That's your formyl carbon and hydrogen. That's not suprising - you're using the C atom type, which you will likely see in atomtypes.atp described as "carbonyl C, peptide backbone". Only if someone really wanted to model a formyl peptide cap would there be a bonded interaction defined from that C type with a hydrogen atom type. Anyway, if you can find a bonded interaction type between H and C atom types that seems to you sufficiently analogous, then you might copy that in ffbonded.itp for the atom types in your molecule. Likewise for angles and dihedrals. Probably you should give up and use acetyl. Mark -- View this message in context: http://gromacs.5086.n6.nabble.com/Diagnoding-system-blowing-up-tp4999804p401.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] Re: Diagnosing + system blowing up
Thanks so much. OK. I'll do my best. Sincerely, Shima - Original Message - From: Mark Abraham To: gmx-users@gromacs.org Cc: Sent: Wednesday, August 1, 2012 2:49 AM Subject: [gmx-users] Re: Diagnosing + system blowing up Shima Arasteh wrote > > Thanks for dear Mark's suggestions. > > What's the typical solution to fix such errors of grompp? > As I've said lots of times, you need to go and look at the atom types you're using, what interactions are defined for them in ffbonded.itp and perhaps reassess those types. Perhaps you can invent some interactions by analogy. Perhaps you can parameterise some. Perhaps you should give up and use acetyl. Shima Arasteh wrote > I don't have any idea to do what, so erased the lines defined in output of > grompp, As Justin said, blindly deleting things is a terrible approach. This assumes that pdb2gmx created interactions that weren't useful to your model physics, given the fact that you've forced it to use atom types that the makers didn't intend. It's much more likely you're doing something wrong than pdb2gmx is doing something wrong. Shima Arasteh wrote > then I went through the NVT equilibrium, it didn't stop by multiple > interaction errors. I don't know what will happen for the rest of the > investigation, put the protein in bilayer and then Umbrella Sampling and > . . No point worrying about that yet. You're trying to run a simulation on a species that your force field didn't anticipate. So you've got to fix that, or choose a different force field, or a different simulation. Shima Arasteh wrote > ERROR 1 [file topol.top, line 414]: > No default Bond types > > And wrote line 414 is : > line 414 of topol.tp: > [bonds] > 1 2 1 > Think about this. grompp couldn't find a bonded interaction of type 1 that matched atoms 1 and 2. That's your formyl carbon and hydrogen. That's not suprising - you're using the C atom type, which you will likely see in atomtypes.atp described as "carbonyl C, peptide backbone". Only if someone really wanted to model a formyl peptide cap would there be a bonded interaction defined from that C type with a hydrogen atom type. Anyway, if you can find a bonded interaction type between H and C atom types that seems to you sufficiently analogous, then you might copy that in ffbonded.itp for the atom types in your molecule. Likewise for angles and dihedrals. Probably you should give up and use acetyl. Mark -- View this message in context: http://gromacs.5086.n6.nabble.com/Diagnoding-system-blowing-up-tp4999804p401.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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 * Only plain text messages are allowed! * 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] Re: Diagnosing + system blowing up
But If I want to use acetyl instead of formyl, then what about the chemical activity of the formyl located in N-terminus? The protein that I will put in the bilayer is composed of 2 monomers . The monomers form a dimer from the N-terminus, the same as gramicidin A channel. Acetyl could be play the same role as formyl here? Sincerely, Shima - Original Message - From: Mark Abraham To: gmx-users@gromacs.org Cc: Sent: Wednesday, August 1, 2012 2:49 AM Subject: [gmx-users] Re: Diagnosing + system blowing up Shima Arasteh wrote > > Thanks for dear Mark's suggestions. > > What's the typical solution to fix such errors of grompp? > As I've said lots of times, you need to go and look at the atom types you're using, what interactions are defined for them in ffbonded.itp and perhaps reassess those types. Perhaps you can invent some interactions by analogy. Perhaps you can parameterise some. Perhaps you should give up and use acetyl. Shima Arasteh wrote > I don't have any idea to do what, so erased the lines defined in output of > grompp, As Justin said, blindly deleting things is a terrible approach. This assumes that pdb2gmx created interactions that weren't useful to your model physics, given the fact that you've forced it to use atom types that the makers didn't intend. It's much more likely you're doing something wrong than pdb2gmx is doing something wrong. Shima Arasteh wrote > then I went through the NVT equilibrium, it didn't stop by multiple > interaction errors. I don't know what will happen for the rest of the > investigation, put the protein in bilayer and then Umbrella Sampling and > . . No point worrying about that yet. You're trying to run a simulation on a species that your force field didn't anticipate. So you've got to fix that, or choose a different force field, or a different simulation. Shima Arasteh wrote > ERROR 1 [file topol.top, line 414]: > No default Bond types > > And wrote line 414 is : > line 414 of topol.tp: > [bonds] > 1 2 1 > Think about this. grompp couldn't find a bonded interaction of type 1 that matched atoms 1 and 2. That's your formyl carbon and hydrogen. That's not suprising - you're using the C atom type, which you will likely see in atomtypes.atp described as "carbonyl C, peptide backbone". Only if someone really wanted to model a formyl peptide cap would there be a bonded interaction defined from that C type with a hydrogen atom type. Anyway, if you can find a bonded interaction type between H and C atom types that seems to you sufficiently analogous, then you might copy that in ffbonded.itp for the atom types in your molecule. Likewise for angles and dihedrals. Probably you should give up and use acetyl. Mark -- View this message in context: http://gromacs.5086.n6.nabble.com/Diagnoding-system-blowing-up-tp4999804p401.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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 * Only plain text messages are allowed! * 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] Re: Diagnosing + system blowing up
On 7/31/12 7:46 PM, Shima Arasteh wrote: But If I want to use acetyl instead of formyl, then what about the chemical activity of the formyl located in N-terminus? The protein that I will put in the bilayer is composed of 2 monomers . The monomers form a dimer from the N-terminus, the same as gramicidin A channel. Acetyl could be play the same role as formyl here? If your reasoning for using a formyl group is for some functionally relevant information, then you need to do the hard work of parameterizing the molecule completely. If you can substitute some other cap (like acetyl) then you have to justify it to a skeptical audience (reviewers). The choice is yours alone. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 * Only plain text messages are allowed! * 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 Force Field Paper including Heme Proteins
Dear gromacs users, We just published a paper titled "Force field development for cofactors in the photosystem II" in Journal of Computational Chemistry, which includes the Amber03 compatible force field for heme-B and works well with heme proteins. You may use it for reference at your convenience. The link for the paper is http://www.ncbi.nlm.nih.gov/pubmed/22685077 Best, Lu -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] Fatal error: Number of grid cells is zero. Probably the system and box collapsed.
Dear gromacs user I did simulation of carbon nanotube (one in center and 6 in the vicinity of that)|: every CNT have 120 atoms. 1) energy minimization 2) equilibration in NVT ensemble when I did equilibration in NPT ensemble, I encountered Fatal error: Number of grid cells is zero. Probably the system and box collapsed. How to solve this problem (with which parameter in the mdp file I can solve this problem)? Is there problem in the force field parameters? If this problem resolves, can I do simulation under these conditions but in the high pressure or tempreture (800 bar or 1800 K)? mdp file for equilibration in NPT ensemble is as follows: title = Yo cpp = /usr/bin/cpp constraints = all-bonds integrator = md dt = 0.001; ps ! nsteps = 5; total (2 ns). nstcomm = 1 nstxout = 100 nstxtcout = 100 nstvout = 100 nstfout = 0 nstlog = 100 nstenergy = 100 nstlist = 10 ns_type = grid rlist = 0.8 rcoulomb= 0.8 rvdw= 0.8 ; Electrostatics coulombtype = Cut-off ; vdw vdwtype = Cut-off ; Berendsen temperature coupling is on in two groups Tcoupl = Nose-Hoover tc-grps= (NUcenter tau_t = 0.10 0.10 ref_t = 1300 1300 ; Energy monitoring energygrps = (NU center ; Isotropic pressure coupling is now on Pcoupl = Parrinello-Rahman Pcoupltype = isotropic tau_p = 1 compressibility = 4.5e-5 ref_p = 1 ; Generate velocites is off at 1300 K gen_vel = no ; Periodic boundary conditions pbc= xyz ; Lincs will write a warning to the stderr if in one step a bond ; rotates over more degrees than lincs-warnangle = 90 ; Non-equilibrium MD freezegrps = (NU center freezedim= N N NY Y Y Any help will highly appreciated. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] Fatal error: Number of grid cells is zero. Probably the system and box collapsed.
On 1/08/2012 1:06 PM, leila karami wrote: Dear gromacs user I did simulation of carbon nanotube (one in center and 6 in the vicinity of that)|: every CNT have 120 atoms. 1) energy minimization 2) equilibration in NVT ensemble when I did equilibration in NPT ensemble, I encountered Fatal error: Number of grid cells is zero. Probably the system and box collapsed. How to solve this problem (with which parameter in the mdp file I can solve this problem)? Standard advice is here http://www.gromacs.org/Documentation/Terminology/Blowing_Up You should pay particular attention to what it says about the use of pressure coupling. Mark Is there problem in the force field parameters? If this problem resolves, can I do simulation under these conditions but in the high pressure or tempreture (800 bar or 1800 K)? mdp file for equilibration in NPT ensemble is as follows: title = Yo cpp = /usr/bin/cpp constraints = all-bonds integrator = md dt = 0.001; ps ! nsteps = 5; total (2 ns). nstcomm = 1 nstxout = 100 nstxtcout = 100 nstvout = 100 nstfout = 0 nstlog = 100 nstenergy = 100 nstlist = 10 ns_type = grid rlist = 0.8 rcoulomb= 0.8 rvdw= 0.8 ; Electrostatics coulombtype = Cut-off ; vdw vdwtype = Cut-off ; Berendsen temperature coupling is on in two groups Tcoupl = Nose-Hoover tc-grps= (NUcenter tau_t = 0.10 0.10 ref_t = 1300 1300 ; Energy monitoring energygrps = (NU center ; Isotropic pressure coupling is now on Pcoupl = Parrinello-Rahman Pcoupltype = isotropic tau_p = 1 compressibility = 4.5e-5 ref_p = 1 ; Generate velocites is off at 1300 K gen_vel = no ; Periodic boundary conditions pbc= xyz ; Lincs will write a warning to the stderr if in one step a bond ; rotates over more degrees than lincs-warnangle = 90 ; Non-equilibrium MD freezegrps = (NU center freezedim= N N NY Y Y Any help will highly appreciated. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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
