No I am using same Gromacs 4.6.5. I run these two simulations again one runs and the other fails with the same .mdp file.
> On 22 Jul 2016, at 13:53, Justin Lemkul <jalem...@vt.edu> wrote: > > > > On 7/22/16 7:50 AM, gozde ergin wrote: >> Dear all, >> >> I use md-vv and SHAKE algorithm however I face an error which I was not >> before. >> Before I had 1-decanol and water system and now I have cis-pionic and water >> system. >> >> I exactly use the same .mdp file just as before however this error comes : >> SHAKE is not supported with domain decomposition and constraint that cross >> charge group boundaries, use LINCS >> >> Do you have any idea why I am getting this error which I was not getting >> before? >> > > Probably you were using a different version of the code before. Various > feature combinations get disabled as suitable tests are not run or bugs are > found. LINCS is more stable, anyway, so just use it instead and the run > should work. > > -Justin > >> MDP FILE: >> >> >> integrator = md-vv >> dt = 0.002 >> nsteps = 8000000 ; 16 ns >> ; Output control >> nstxout = 2000 >> nstvout = 2000 >> nstlog = 2000 >> nstenergy = 2000 >> ; Bond parameters >> continuation = no ; Initial simulation >> constraint_algorithm = shake ; holonomic constraints >> constraints = all-bonds ; all bonds (even heavy atom-H bonds) >> constrained >> shake_tol = 0.0001 >> ; Neighborsearching >> ns_type = grid ; search neighboring grid cels >> nstlist = 5 ; 10 fs >> rlist = 1.2 ; short-range neighborlist cutoff (in nm) >> rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm) >> rvdw = 1.2 ; short-range van der Waals cutoff (in nm) >> ; Electrostatics >> coulombtype = PME ; Particle Mesh Ewald for long-range >> electrostatics >> pme_order = 4 ; cubic interpolation >> fourierspacing = 0.16 ; grid spacing for FFT >> ; Temperature coupling >> ; tcoupl is implicitly handled by the sd integrator >> tcoupl = nose-hoover >> tc-grps = System >> tau_t = 1.0 >> ref_t = 300 >> ; Periodic boundary conditions >> pbc = xyz ; 3-D PBC >> ; Dispersion correction >> DispCorr = EnerPres ; account for cut-off vdW scheme >> ; Velocity generation >> gen_vel = yes ; Velocity generation is on >> gen_temp = 300 ; temperature for velocity generation >> gen_seed = -1 ; random seed >> ; COM motion removal >> ; These options remove COM motion of the system >> nstcomm = 10 >> comm-mode = Linear >> comm-grps = System >> >> >> >> thanks >> > > -- > ================================================== > > 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. -- 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.
