[gmx-users] Simulation of Small Water Box
Dear Users Can Anybody help me to simulate a water box with nearly 14.45 A box size and approximately 93 water molecules. I have tried to simulate it using the 'spc' water model. I have done the SD and CG minimization step. Till that step it was fine, but when I tried to do MD then I got the following error message *One of the box vectors has become shorter than twice the cut-off length or box_yy-|box_zy| or box_zz has become smaller than the cut-off.* Is there any well established method to simulate a small water box nearly of the size I have mentioned? It would be great if I could get it. Have a nice day. -- With Regards Monoj Mon Kalita Institute of Biophotonicshttp://www.ym.edu.tw/biophotonics/eng_version/home.htm National Yang-Ming Universityhttp://nymu-e.web.ym.edu.tw/front/bin/home.phtml Taipei, Taiwan -- 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] invalid pairstype 180
1 16 331 19 271 27 331 [ angles ] ; ai aj ak funct angle fc 3242120.00 390.00 32 182120.00 390.00 42 182120.00 560.00 2452120.00 560.00 24 232120.00 560.00 54 232125.00 750.00 4562121.00 685.00 4572115.00 610.00 6572124.00 730.00 5782116.00 465.00 5792125.00 750.00 8792115.00 460.00 79 102110.00 1280.00 79 132120.00 560.00 109 132125.00 750.00 9 10 112116.00 465.00 9 10 122115.00 460.00 11 10 122109.50 285.00 9 13 142109.50 285.00 16 15 172120.00 560.00 16 15 272120.00 560.00 17 15 272120.00 560.00 15 16 182120.00 560.00 15 16 252125.00 750.00 18 16 252120.00 560.00 15 17 192132.00 760.00 15 17 332126.00 640.00 19 17 332105.00 1320.00 2 18 162120.00 560.00 2 18 312120.00 560.00 16 18 312120.00 560.00 17 19 202126.00 575.00 17 19 212111.00 530.00 20 19 212120.00 505.00 19 21 222106.00 1690.00 1 22 212119.00 1210.00 1 22 332125.00 750.00 21 22 332112.00 1400.00 4 23 242120.00 390.00 4 23 252120.00 560.00 24 23 252120.00 390.00 16 25 232120.00 560.00 16 25 262120.00 390.00 23 25 262120.00 390.00 15 27 282120.00 390.00 15 27 292120.00 560.00 28 27 292120.00 390.00 27 29 302120.00 390.00 27 29 312120.00 560.00 30 29 312120.00 390.00 18 31 292120.00 560.00 18 31 322120.00 390.00 29 31 322120.00 390.00 17 33 222108.00 465.00 17 33 342131.00 927.00 22 33 342121.40 690.00 [ dihedrals ] ; GROMOS improper dihedrals ; ai aj ak al funct angle fc 15 27 29 312 0.00 167.36 27 29 31 182 0.00 167.36 29 31 18 162 0.00 167.36 31 18 16 152 0.00 167.36 18 16 15 272 0.00 167.36 16 15 27 292 0.00 167.36 17 19 21 222 0.00 167.36 19 21 22 332 0.00 167.36 21 22 33 172 0.00 167.36 22 33 17 192 0.00 167.36 33 17 19 212 0.00 167.36 16 25 2342 0.00 167.36 25 23422 0.00 167.36 2342 182 0.00 167.36 42 18 162 0.00 167.36 2 18 16 252 0.00 167.36 18 16 25 232 0.00 167.36 15 16 17 272 0.00 167.36 16 15 18 252 0.00 167.36 17 15 19 332 0.00 167.36 27 15 28 292 0.00 167.36 182 16 312 0.00 167.36 25 16 23 262 0.00 167.36 31 18 29 322 0.00 167.36 234 182 0.00 167.36 29 27 30 312 0.00 167.36 234 24 252 0.00 167.36 425 232 0.00 167.36 33 17 22 342 0.00 167.36 19 17 20 212 0.00 167.36 54672 0.00 167.36 97 10 132 0.00 167.36 75892 0.00 167.36 221 21 332 0.00 167.36 [ dihedrals ] ; ai aj ak al functph0 cp mult 24571180.0033.502 45791180.0033.502 579 131180.0033.502 139 10 111180.0033.502 79 13 141180.0033.502 16 15 17 331180.00 1.532 [ exclusions ] ; ai aj funct ; GROMOS 1-4 exclusions 1 17 1 19 1 34 2 15 2 24 2 25 2 29 2 32 35 3 16 3 23 3 31 4 16 4 26 4 31 5 18 5 24 5 25 15 20 15 21 15 22 15 23 15 26 15 30 15 31 15 34 16 24 16 28 16 29 16 32 17 18 17 25 17 28 17 29 18 23 18 26 18 27 18 30 19 34 20 22 20 33 21 34 24 26 25 27 25 31 27 32 28 30 28 31 30 32 -- With Regards Monoj Mon Kalita Institute of Biophotonicshttp
[gmx-users] How to include a small organic molecule
Dear Gromacs Users I am new to this mailing list. I am trying to include a small molecule into lipid bilayer patch which already have another protein molecule. When I google it then I found a method in the Swissparam website. But, there it is mentioned how to do that with Charm27 forcefield, and how to generate the topology file with Charm27 forcefield. But, my idea is to do this with gromos45a3 forecfield. However I have tried the method with charm27 forcefield, I have edited the atomtype.itp and aminoacids.rtp files in the root folder. But, when I tried to proceed for SD step with grompp then one error message is showing which is Fatal Error: Syntax error - File Ligand.itp, line 7, Last line read : '[ atomtypes]' Invalid order for directive atomtypes. My input file order in the topology file is ;include forcefield paramaeters #include chram27/forecefield.itp #include popc.itp #include ligand.itp . [molecules] ;compound #mols Protein_chain_A 1 POPC 276 ligand 1 SOL 8748 Kindly have a look, and if possible let me know how to proceed with gromos45a3 forcefield. -- With Regards Monoj Mon Kalita Institute of Biophotonicshttp://www.ym.edu.tw/biophotonics/eng_version/home.htm Fischer's Lab http://www.ym.edu.tw/%7Ewfischer/group_mon.htm National Yang-Ming Universityhttp://nymu-e.web.ym.edu.tw/front/bin/home.phtml Taipei, Taiwan mon.123c...@gmail.com +886-978014883 -- 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
