Hello Gromacs users:
I am running a dimeric protein simulation on Gromacs 3.3 using the force filed G43a1. For initially minimizing the hydrogen i did some small minimization and equilibration in the vacuum by maintaining the restraints then i added ions and water but in the very first minimization i m getting the following error 1-4 interaction between 1 and 9 at distance 8.454 which is larger than the 1-4 table size 1.000 nm These are ignored for the rest of the simulation This usually means your system is exploding, In the log file i am getting : 4 inconsistent shifts check your topology following is my input file : title = 1min in water define = -DPOSRES integrator = steep dt = 0.001 constraints = none nsteps = 500 nstlist = 10 rcoulomb = 1 rlist = 1 rvdw = 1.4 ns_type = grid coulombtype = PME pbc = xyz gen_vel = no fourierspacing = 0.12 pme_order = 6 ewald_rtol = 1e-5 optimize_fft = yes comm_mode = angular emtol = 100.0 emstep = 0.01 after adding the ions i have modified the topology file, please tell me what is the exact reason for this error or what are the other things i should check in relation to the error With regards Thanks On 7/2/07, Tsjerk Wassenaar <[EMAIL PROTECTED]> wrote:
Hi Fufeng Liu, I guess you ran pdb2gmx on the two peptides, where both peptides had the same chain identifiers. In that case, pdb2gmx will assume that it's one molecule and connect them. Use chain identifiers to indicate the different peptides, or build topologies first on separate files and combine the peptides later. Cheers, Tsjerk On 7/1/07, Mark Abraham <[EMAIL PROTECTED]> wrote: > Please keep requests for help on the list. That way they're archived for > others to use, and other people can raise points of interest. > > The last sentence here > http://wiki.gromacs.org/index.php/Errors#1-4_interaction_not_within_cut-off > is my suggestion for you :-) Probably, you have only one [molecule] > statement for your two molecules, and by chance you included it first so > that there was no error message from grompp. If you don't understand why > this is a problem, find the relevant section of Chapter 5 of the manual - > or read the whole lot of that chapter! :-) > > Mark > > ---------------------------- Original Message ---------------------------- > Subject: How simulate two peptides in a box? > From: [EMAIL PROTECTED] > Date: Sun, July 1, 2007 11:09 pm > To: [EMAIL PROTECTED] > -------------------------------------------------------------------------- > > Dear Mark: > I'm a graduate student at Tianjin University. I want to simulate two > peptides > in a box using GROMACS software? I followed your suggestion > > {set up your topologies (suggest one molecule in each of two .itp files) > #include them in the .top file, pick a starting configuration for both of > them in the same structure file, solvate, minimize.} > > But when I minimized the system, I got the information ¡±1-4 interaction > between 83 and 85 at distance 1.862 which is larger than the 1-4 table > size 1.000 nm¡±. I checked the topology and found that atom 83 belong to > one peptide and the atom 85 the other peptide. That¡¯s to say the two > peptides were considered as a peptide. Can you tell me how to do? I'd be > very happy and grateful if you could tell me how to do it. > Looking forward to your reply. > Best regards. > Fufeng Liu > > > > > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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