Thank you Justin for Your Help, and advice, i have already the modification on the nvt.mdp that you suggest, but the problem is still there, my system has about 150.000 atoms , and for the energy minization i used DFLEXIBLE, and emtol was ajusted to 1000, i take a look to the steep0.pdb that gromacs produce, and there are atoms out of the box, but the DOX molecule is OK
what would you suggest? - a emtol lower? - a water and dox md? ( maybe the DOX.itp can be the problem) ? Thank you Justin, Andres > Date: Sat, 15 Mar 2014 14:23:15 -0400 > From: [email protected] > To: [email protected] > Subject: Re: [gmx-users] NVT problem > > > > On 3/15/14, 2:19 PM, Andres Ortega wrote: > > HI , Dear Gromacs Users, > > > > I´ve been trying to run a NVT simulation, in order to equilibrate my system( > > POPC + IONCHANNEL + SOL_IONS and DOX( Drug Molecule), i have already run a > > EM, with DFLEXIBLE, and when i´m trying to run the NVT.mdp, the usual > > comment of Water cannot be settle appear > > > > and this > > > > Step 1, time 0.002 (ps) LINCS WARNING > > relative constraint deviation after LINCS: > > rms 417295953701.842102, max 94388491386880.000000 (between atoms 7122 and > > 7123) > > bonds that rotated more than 30 degrees: > > > > according with previous post, this could be of a problem of the topol (DOX) > > or problems with my mdp file, this is my .mdp , i was wondering if you could > > help me and give me some advices to solve this > > > > Thanks in advance for your time and attention , Andres Ortega > > > > title = NVT equilibration for channel_dox > > define = -DPOSRES -DPOSRES_DOX ; position restrain the protein > > and for DOX > > ; Run parameters > > integrator = md ; leap-frog integrator > > nsteps = 5000000 ; 2 * 500000 = 1 ns ;10ns > > dt = 0.002 ; 2 fs > > > > cutoff-scheme = verlet ; > > > > ; Output control > > nstxout = 1000 ; save coordinates every 2 ps > > nstvout = 1000 ; save velocities every 2 ps > > nstenergy = 1000 ; save energies every 2 ps > > nstlog = 1000 ; update log file every 2 ps > > > > ; Bond parameters > > continuation = no ; first dynamics run > > constraint_algorithm = lincs ; holonomic constraints > > constraints = all-bonds ; all bonds (even heavy atom-H bonds) > > constrained > > lincs_iter = 1 ; accuracy of LINCS > > lincs_order = 4 ; also related to accuracy > > ; Neighborsearching > > ns_type = grid ; search neighboring grid cels > > nstlist = 10 ; 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 is on > > tcoupl = V-rescale ; modified Berendsen > > thermostat > > tc-grps = Protein POPC DOX Water_and_ions ; three > > coupling groups - more > > accurate > > tau_t = 0.1 0.1 0.1 0.1 ; time > > constant, in ps > > ref_t = 310 310 310 310 ; > > reference temperature, one for each > > group, in K > > ; Pressure coupling is off > > pcoupl = no ; no pressure coupling in NVT > > ; Periodic boundary conditions > > pbc = xyz ; 3-D PBC > > ; Dispersion correction > > DispCorr = EnerPres ; account for cut-off vdW scheme > > ; Velocity generation > > gen_vel = yes ; assign velocities from Maxwell > > distribution > > gen_temp = 310 ; temperature for Maxwell distribution > > gen_seed = -1 ; generate a random seed > > ; COM motion removal > > ; These options remove motion of the protein/bilayer relative to the > > solvent/ions > > nstcomm = 1 > > comm-mode = Linear > > comm-grps = Protein_POPC DOX Water_and_ions > > > > Specifying DOX as separately in both tc-grps and comm-grps is the most > probable > source of error. It is too small to justify its own thermostat, and > certainly > should not have its COM motion removed separately. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA 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 > > [email protected] | (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 [email protected]. -- 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 [email protected].
