[gmx-users] -rcon parameter in mdrun - what values have sense?
Hi, I constructed some (about 200 atoms) molecule, have got itp and gro files for it using PRODRG server and put it in water box. Short test run was O'K. But when I tried long run I have got message: after about 1.5ns time: -- DD cell 0 1 0: Neighboring cells do not have atoms: 73 DD cell 0 3 0: Neighboring cells do not have atoms: 50 49 Program mdrun, VERSION 4.5.5 Source code file: domdec_con.c, line: 693 Fatal error: DD cell 0 1 0 could only obtain 43 of the 44 atoms that are connected via constraints from the neighboring cells. This probably means your constraint lengths are too long compared to the domain decomposition cell size. Decrease the number of domain decomposition grid cells or lincs-order or use the -rcon option of mdrun. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- I do not know where I can 1) "...decrease the number of domain decomposition grid cells or 2) decrease lincs-order". 3) I can use -rcon option of mdrun. In this case I understand how I can change this parameter but I don't know what are the reasonable values for it. Is it 0.761A at the beginning of my calculation (see below)? Should I try to make it shorter or longer? It looks that from one hand I should make it longer but from another hand it should be less than minimum cell size (0.898 in my case? see below) I have next information about domain decomposition in the beginning of run: - Initializing Domain Decomposition on 64 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: 0.817 nm, LJ-14, atoms 138 148 multi-body bonded interactions: 0.817 nm, Proper Dih., atoms 148 138 Minimum cell size due to bonded interactions: 0.898 nm Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.761 nm Estimated maximum distance required for P-LINCS: 0.761 nm Using 32 separate PME nodes Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25 Optimizing the DD grid for 32 cells with a minimum initial size of 1.123 nm The maximum allowed number of cells is: X 5 Y 5 Z 5 Domain decomposition grid 4 x 4 x 2, separate PME nodes 32 PME domain decomposition: 4 x 8 x 1 Interleaving PP and PME nodes This is a particle-particle only node - Any ideas what to do? Thank you in advance. Alex -- 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] construction of homopolymer from non-standard monomers in gromacs
Hi, I am trying construct homopolymer from non-standard monomers . I have pdb, itp and gro files for monomer and constructed pdb file for polymer. I can put them in corresponding top/forcefield.ff directory. But how I can get itp and gro files for polymer (for example, for 3-mer in simplest case)? How Gromacs knows which atoms are "head" and "tail" atoms for connection of monomers into polymer (like in "Material Studio")? Thank you in advance. Igor -- 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[2]: 回复： [gmx-users] No such moleculetype Na
Change name Cl to name CL and check name Na in forcefield you use (it could be NA). 11 декабря 2011, 17:30 от Mark Abraham : On 11/12/2011 11:43 PM, yp sun wrote: The name of ion is different when using different force field You can check which field force you use and find out how Na and Cl ion is written in this force field. The molecule name is constant over all force fields in the 4.5 series of GROMACS, and the molecule name is all that genion cares about. Atom and residue names might vary. Mark Yeping Sun CAS Key Laboratory of Pathogenic Microbiology & Immunology INSTITUTE OF MICROBIOLOGY CHINESE ACADEMY OF SCIENCES NO.1 Beichen West Road,Chaoyang District,Beijing 100101,china --- 11年12月11日，周日, Setare Jiji 写道： 发件人: Setare Jiji 主题: [gmx-users] No such moleculetype Na 收件人: gmx-users@gromacs.org 日期: 2011年12月11日,周日,下午5:17 Hi, Thanks for your responding. I checked my ions.itp file in which file sodium and chlorine ions are as Na and Cl form. Thus, I used genion as follows: genion -s ions.tpr -o 1AKI_solv_ions.gro -p topol.top -nname Cl -nn 8 -pname Na Unfortunately, I encountered same fatal error. any help will highly appreciated. -下面为附件内容- -- gmx-users mailing list 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. 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 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
