Re: [gmx-users] Graphene sheet topology
Did you try googling "gromacs graphene topology" or "gromacs cnt topology"? To refine the interactions in existing tutorials, I actually wrote a paper a while back: http://iopscience.iop.org/article/10.1088/0957-4484/25/48/485701/meta -- which noone seems to cite. :) Improper dihedrals are generated automatically by programs like x2top, but whether they are necessary actually depends on how you build the graphene model, including how many dihedrals per C-C bond. If you run x2top with -alldih, all dihedrals will be converted to proper dihedrals. Alex On 3/17/2018 12:30 PM, Mostafa Fakhraee wrote: Hi, Does anyone know how to build a graphene topology based on OPLS-AA force field? Also is it possible to let me know how can I determine the improper dihedral of graphene because graphene sheet has a lot of dihedrals and it is difficult for do that manually? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Graphene sheet topology
Thanks Justin as always for your prompt reply. I have now created the graphene topology the way u suggested that is I issued the following command 1. g_x2top -f file.gro -o graphene.top -pbc: I did not prefer to use the -noparam option since it does not print the k0, k1 and similar values. 2. I have now started the simulation with all my mdp files (ions.mdp, minim.mdp, nvt.mdp, npt.mdp and md.mdp) containing the "periodic molecules=yes" line and as of now the simulation is running fine. But the last one crashed around 25 ns showing the Lincs warnings and stuffs so keeping my fingers crossed. 3. I am keeping the dihedral function type 1 as per your suggestion. Please let me know if what I am doing right now as mentioned above makes sense or not. I will update on the outcomes of my simulation even if everything goes right. Thanks once again for the reply Justin..:) Soumadwip Ghosh Senior Research Fellow Indian Institute of Technology Bombay India -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Graphene sheet topology
On 4/23/16 1:37 AM, soumadwip ghosh wrote: Hello all, I am currently working on the interaction between a flat graphene sheet and nucleic acids at various physiological conditions. I am using CHARMM 27 force field and GROMACS 4.5.6 for MD simulations. Here is my work order 1. I created a graphene.top file according to the tutorial by Andrea Minoia. 2. I went upto NPT equilibration without any problem but my MDrun crashes printing the following error (I modified the .n2t and other CHARMM 27 forcefield files according to the tutorial) Fatal error: 25 particles communicated to PME node 4 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x. This usually means that your system is not well equilibrated. From the mails in the mailing list I am assuming that my graphene topology has something terribly bad since I have worked with the particular nucleic acid in CHARMM27 and it does not have any issue. I am uploading the pdb and itp files of my graphene sheet followed by the md.mdp and md.log file. Any kind of help to troubleshoot this error would be greatly appreciated. pdb file of graphene: https://drive.google.com/open?id=0B7SBnQ5YXQSLQWVod3psQTFwSzg graphene.itp: https://drive.google.com/open?id=0B7SBnQ5YXQSLTXlqci1aX3NzU3c the visualization of graphene.pdb: https://drive.google.com/open?id=0B7SBnQ5YXQSLMExiSG5GR3VIMjA My md.mdp file: https://drive.google.com/open?id=0B7SBnQ5YXQSLMmd1di1jbHpubFE the md.log file I obtained: https://drive.google.com/open?id=0B7SBnQ5YXQSLdXZDZVNDOFJqVDg PS: I forgot to issue the -pbc while executing the g_x2top command and also did not change the dihedral function type from 1 to 3 as suggested in the tutorial. Can this be a reason for the above error to occur? Your sheet appears to be periodic, so yes, you need to treat it as such (also by adding "periodic_molecules = yes" in the .mdp file). Otherwise, your atoms are at very close distance at the box edges and things explode. CHARMM uses periodic dihedrals, so the function type is 1 (though we usually use 9 because CHARMM often applies multiple terms to each dihedral). But if you only have one multiplicity per dihedral, type 1 is fine (and setting it to 9 would be equivalent in this case). -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Graphene sheet topology
Hello all, I am currently working on the interaction between a flat graphene sheet and nucleic acids at various physiological conditions. I am using CHARMM 27 force field and GROMACS 4.5.6 for MD simulations. Here is my work order 1. I created a graphene.top file according to the tutorial by Andrea Minoia. 2. I went upto NPT equilibration without any problem but my MDrun crashes printing the following error (I modified the .n2t and other CHARMM 27 forcefield files according to the tutorial) Fatal error: 25 particles communicated to PME node 4 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x. This usually means that your system is not well equilibrated. >From the mails in the mailing list I am assuming that my graphene topology has something terribly bad since I have worked with the particular nucleic acid in CHARMM27 and it does not have any issue. I am uploading the pdb and itp files of my graphene sheet followed by the md.mdp and md.log file. Any kind of help to troubleshoot this error would be greatly appreciated. pdb file of graphene: https://drive.google.com/open?id=0B7SBnQ5YXQSLQWVod3psQTFwSzg graphene.itp: https://drive.google.com/open?id=0B7SBnQ5YXQSLTXlqci1aX3NzU3c the visualization of graphene.pdb: https://drive.google.com/open?id=0B7SBnQ5YXQSLMExiSG5GR3VIMjA My md.mdp file: https://drive.google.com/open?id=0B7SBnQ5YXQSLMmd1di1jbHpubFE the md.log file I obtained: https://drive.google.com/open?id=0B7SBnQ5YXQSLdXZDZVNDOFJqVDg PS: I forgot to issue the -pbc while executing the g_x2top command and also did not change the dihedral function type from 1 to 3 as suggested in the tutorial. Can this be a reason for the above error to occur? Thanks and regards, Soumadwip Ghosh Senior Research Scholar Indian Institute of Technology Bombay India -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
