yes it worked. i only added CA CA CZ CZ 0.000 0.000 0.000 0.000 in diheadral block. since all 12 errors point the same kind of diheadral type.
Then i tried to mdrun...i got this error message.... Fatal error: 1 particles communicated to PME node 6 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension y. This usually means that your system is not well equilibrated. so i followed the energy minimization steps given in the lysozyme tutorial... and ended up with vales like below... Steepest Descents converged to Fmax < 1000 in 56 steps Potential Energy = 8.3839850e+02 Maximum force = 9.7320355e+02 on atom 206 Norm of force = 1.8842863e+02 there you have clearly stated that the potential energy should be in range of e-5 to e-6. but mine is ~+1000. i played with emsteps and nsteps. but still am getting the same potential energy. could you please help me out with this? Thank you! minimum.mdp i used-( taken from your lysozyme tutorial) minim.mdp - used as input into grompp to generate em.tpr ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1000.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm emstep = 0.0001 ; Energy step size nsteps = 50000000 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1.0 ; Frequency to update the neighbor list and long range forces ns_type = grid ; Method to determine neighbor list (simple, grid) rlist = 1.0 ; Cut-off for making neighbor list (short range forces) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb = 1.0 ; Short-range electrostatic cut-off rvdw = 1.0 ; Short-range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions (yes/no) ~ Sidath On Tue, Feb 4, 2014 at 8:49 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 2/3/14, 10:14 PM, Sidath Wijesinghe wrote: > >> Justin,, >> >> i rechecked the opls/ff that i used and found some errors, after >> correction them >> i got the .top file. >> note that i was able to define the charge groups as well. when i use this >> .top >> file with grompp, >> now am getting 12 errors...as follwos.. >> >> >> ERROR 1 [file topol.top, line 1399]: >> No default Ryckaert-Bell. types >> >> >> ERROR 2 [file topol.top, line 1400]: >> No default Ryckaert-Bell. types >> >> >> ERROR 3 [file topol.top, line 1415]: >> No default Ryckaert-Bell. types >> >> >> ERROR 4 [file topol.top, line 1416]: >> No default Ryckaert-Bell. types >> and so on... >> >> i did the mapping as you suggested,as an example line 1399 in .top >> as follwos... >> 2 1 82 81 3 ( here 2 1 82 & 81 are carbon atoms) >> >> and the mapping to all 12 errors.....then modified the ffbonded.itp >> file's >> diheadral block as follows... >> >> C2 C1 C82 C81 3 0.00 0.00 0.00 0.00 >> >> so on.... >> >> then bond tyype block as follows.... >> >> C2 C1 1 0.00 0.00... so on.... >> >> added those atom types in atomtypes.atp like below... >> C1 >> C2 >> C3 >> C4 >> C11 >> C12 >> C13................so on >> >> after that when i do grompp gives me a fatal error like >> >> Program grompp, VERSION 4.5.5 >> Source code file: toppush.c, line: 631 >> >> Fatal error: >> Unknown bond_atomtype C1 >> >> could you please tell me what i have done wrong? >> >> > You used atom names, not atom types. In [atoms] in your .top, each atom > type is assigned as opls_XXX. Looking in ffnonbonded.itp, the second > column of the corresponding opls_XXX type is its bonded type equivalent. > That is the identifier you need to be using. The force field doesn't care > what atoms are named, but it does care what type they are. > > > and at the same time....i tied delete those 12 lines in .top and do >> grompp...it >> worked....but when i >> did mdrun.....i am getting the signs of blowing up system....what i can >> do over >> here....how can i get rid of these errors >> and carry out my simulation? >> >> > Of course if you delete an essential bonded interaction, the simulation > will go haywire. Deletion may be convenient for getting grompp to shut up, > but it's not sound practice. > > -Justin > > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > 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. > -- Sidath Wijesinghe Graduate Teaching Assistant Dept Of Chemistry Clemson University -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? 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