Thanks a lot,
Best regards On Sun, Jan 14, 2018 at 5:32 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 1/14/18 11:29 AM, Faezeh Pousaneh wrote: > >> Thank you Justin, now I understood. However, I do not have any target data >> for my system. What do you suggest? the longer rcoulomb is safer, right? >> > > Not necessarily. Longer cutoffs do not imply greater accuracy, nor does > any specific value. It depends on your model. You have to demonstrate to a > skeptical audience that your methods are sound. That requires describing a > known system and its structure, energetics, and dynamics. Then you can move > to predicting unknowns. Without that, there's no control to determine if > your work is meaningful or a random number generator. > > > -Justin > > >> Best regards >> >> >> On Sun, Jan 14, 2018 at 4:47 PM, Justin Lemkul <jalem...@vt.edu> wrote: >> >> >>> On 1/14/18 10:42 AM, Faezeh Pousaneh wrote: >>> >>> Thanks Justin. But I only define vdW potential form, coulomb potential >>>> form >>>> is as in Gromacs. So I would like to have electrostatic interactions as >>>> other systems, so are >>>> >>>> rlist = 0.9 (in nm) >>>> rcoulomb = 0.9 (in nm) >>>> >>>> fine while I am using PME? >>>> >>>> Again, there is no standard value here and it is dictated by the >>> functional form being used. You have a custom interaction potential, even >>> if you're using normal PME alongside you have user-defined, tabulated vdW >>> interactions. Presumably there should be some evaluation of what cutoffs >>> are used to satisfy whatever the assumptions are in the parametrization >>> of >>> your model, i.e. you need to have some target data of a known system that >>> tells you that your physical model (cutoffs and functional form) is >>> right, >>> and then you use those same settings in whatever systems are of interest. >>> >>> -Justin >>> >>> >>> Best regards >>> >>>> >>>> On Sun, Jan 14, 2018 at 3:46 PM, Justin Lemkul <jalem...@vt.edu> wrote: >>>> >>>> >>>> On 1/14/18 6:01 AM, Faezeh Pousaneh wrote: >>>>> >>>>> Hi, >>>>> >>>>>> I have a system of charged hard spheres (user-potential), where the >>>>>> vdW >>>>>> cut-off should be diameter of my molecule 0.3479. I wonder if I chose >>>>>> rlist >>>>>> and rcoulomb correctly? (see below please) >>>>>> >>>>>> I'm not sure if anyone can tell you that. You're using custom >>>>>> >>>>> potentials, >>>>> so setting cutoffs is part of the parametrization of that potential >>>>> itself. >>>>> >>>>> -Justin >>>>> >>>>> >>>>> integrator = md >>>>> >>>>> dt = 0.001 >>>>>> nsteps = 30000000 >>>>>> nstxout = 100000 ; save coordinates >>>>>> every 0 >>>>>> ps >>>>>> nstvout = 100000 ; save velocities >>>>>> every >>>>>> 0 >>>>>> ps >>>>>> nstlog = 100000 ; update log file >>>>>> every >>>>>> nstenergy = 100000 ; save energies every >>>>>> nstxtcout = 100000 ; Output frequency for >>>>>> xtc >>>>>> file >>>>>> xtc-precision = 100000 ; precision for xtc file >>>>>> ns_type = grid ; search neighboring grid >>>>>> cells >>>>>> nstlist = 10 ; fs >>>>>> pbc = xyz ; 3-D PBC >>>>>> rlist = 0.9 ; short-range >>>>>> neighbor-list >>>>>> cutoff (in nm) >>>>>> rcoulomb = 0.9 ; short-range >>>>>> electrostatic >>>>>> cutoff >>>>>> (in nm) >>>>>> rvdw = 0.3479 ; short-range van der >>>>>> Waals >>>>>> cutoff >>>>>> (in nm) >>>>>> coulombtype = PME-user ; Particle Mesh Ewald >>>>>> for >>>>>> long-range electrostatics >>>>>> pme_order = 4 ; cubic interpolation >>>>>> fourierspacing = 0.16 ; grid spacing for FFT >>>>>> vdw-type = user >>>>>> Tcoupl = berendsen ; modified Berendsen >>>>>> thermostat >>>>>> tc-grps = co2 rest ; two coupling >>>>>> groups - >>>>>> more accurate >>>>>> tau_t = 0.1 0.1 ; time constant, in ps >>>>>> ref_t = 179.8 179.8 ; reference temperature, >>>>>> one >>>>>> for >>>>>> each group, in K >>>>>> ;tc-grps = system >>>>>> cutoff-scheme =group >>>>>> energygrps = co2 rest >>>>>> Pcoupl = berendsen ;Parrinello-Rahman >>>>>> Pcoupltype = Isotropic >>>>>> tau_p = 1.0 >>>>>> compressibility = 6.2e-5 >>>>>> ref_p = 5500.0 >>>>>> gen_vel = yes >>>>>> gen_temp = 179.8 >>>>>> gen_seed = 712349 >>>>>> DispCorr =no; EnerPres ; account for cut-off >>>>>> vdW >>>>>> scheme >>>>>> constraints = all-bonds ; all bonds constrained >>>>>> (fixed >>>>>> length) >>>>>> continuation = no ; Restarting after NPT >>>>>> constraint-algorithm = lincs ; holonomic constraints >>>>>> lincs_iter = 1 ; accuracy of LINCS >>>>>> lincs_order = 4 ; also related to accuracy >>>>>> Best regards >>>>>> >>>>>> -- >>>>>> >>>>> ================================================== >>>>> >>>>> Justin A. Lemkul, Ph.D. >>>>> Assistant Professor >>>>> Virginia Tech Department of Biochemistry >>>>> >>>>> 303 Engel Hall >>>>> 340 West Campus Dr. >>>>> Blacksburg, VA 24061 >>>>> >>>>> jalem...@vt.edu | (540) 231-3129 >>>>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html >>>>> >>>>> ================================================== >>>>> >>>>> -- >>>>> 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. >>>>> >>>>> >>>>> -- >>> ================================================== >>> >>> Justin A. Lemkul, Ph.D. >>> Assistant Professor >>> Virginia Tech Department of Biochemistry >>> >>> 303 Engel Hall >>> 340 West Campus Dr. >>> Blacksburg, VA 24061 >>> >>> jalem...@vt.edu | (540) 231-3129 >>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html >>> >>> ================================================== >>> >>> -- >>> 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. >>> >>> > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.biochem.vt.edu/people/faculty/JustinLemkul.html > > ================================================== > > -- > 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? 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