Thank you very much for the links! Best regards, Mahsa
On Mon, Sep 18, 2017 at 1:30 AM, Dallas Warren <dallas.war...@monash.edu> wrote: > These two images will help you see what is going on: > > https://twitter.com/dr_dbw/status/909559339366572032 - shows a > molecule that appears to be outside the box. > > https://twitter.com/dr_dbw/status/909559783291723776 - however, that > molecule actually enters through the opposite face of the box. > Catch ya, > > Dr. Dallas Warren > Drug Delivery, Disposition and Dynamics > Monash Institute of Pharmaceutical Sciences, Monash University > 381 Royal Parade, Parkville VIC 3052 > dallas.war...@monash.edu > --------------------------------- > When the only tool you own is a hammer, every problem begins to resemble a > nail. > > > On 18 September 2017 at 09:22, Mahsa E <ebadi.ma...@gmail.com> wrote: > > Thank you for you quick reply, Justin and Dallas! Very good point! > > > > Best regards, > > Mahsa > > > > > > > > > > > > On Mon, Sep 18, 2017 at 1:00 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > >> > >> > >> On 9/17/17 6:57 PM, Mahsa E wrote: > >> > >>> Could you please see the link below for the input and output simulation > >>> box: > >>> > >>> https://www.dropbox.com/sh/kb36ake7mj5iovh/AABPF4_ > FUfvSPZxdO5WN3JnEa?dl=0 > >>> > >>> > >>> Actually, I thought since some of the chains went out of the simulation > >>> box, then density have been changed. In my previous experience with > >>> another > >>> polymer, I didn't see this difference in the systems after the > production > >>> run, so I'm wondering if this is related to the stability of the > system? > >>> > >>> > >> As Dallas said, this is just a periodicity/visualization effect - > there's > >> no such thing as "outside" a periodic cell. > >> > >> Your "before MD" has "broken" molecules, i.e. all the atoms are > visualized > >> as being in the central image. Your "after MD" is just those molecules > >> made whole. If you make the initial frame whole (trjconv -pbc whole), > you > >> will see a similar configuration. > >> > >> -Justin > >> > >> > >> Best regards, > >>> Mahsa > >>> > >>> > >>> > >>> > >>> > >>> On Mon, Sep 18, 2017 at 12:10 AM, Dallas Warren < > dallas.war...@monash.edu > >>> > > >>> wrote: > >>> > >>> Because that is how the system changed within the simulation time? > >>>> > >>>> What exactly is the problem as you see it, and why do you think it is > a > >>>> problem? > >>>> > >>>> And remember, you have a periodic boundary condition that means the > >>>> one edge of the box wraps around to the opposite one. So "out of the > >>>> box" is a visualisation artefact, not a "problem". > >>>> http://www.gromacs.org/Documentation/Terminology/ > >>>> Periodic_Boundary_Conditions > >>>> Catch ya, > >>>> > >>>> Dr. Dallas Warren > >>>> Drug Delivery, Disposition and Dynamics > >>>> Monash Institute of Pharmaceutical Sciences, Monash University > >>>> 381 Royal Parade, Parkville VIC 3052 > >>>> dallas.war...@monash.edu > >>>> --------------------------------- > >>>> When the only tool you own is a hammer, every problem begins to > resemble > >>>> a > >>>> nail. > >>>> > >>>> > >>>> On 18 September 2017 at 06:31, Mahsa E <ebadi.ma...@gmail.com> wrote: > >>>> > >>>>> Dear gmx-users, > >>>>> > >>>>> I did a 200 ns production md run in NVT ensemble for a simulation > box of > >>>>> polymer chains. Before this step, I did the energy minimisation, NVT > and > >>>>> NPT equilibration on the system. The problem is after the production > >>>>> > >>>> run, I > >>>> > >>>>> don't get the initial equilibrated packed box of polymer and it seems > >>>>> > >>>> more > >>>> > >>>>> like a circular shape with some parts of the chains out of the box. > What > >>>>> > >>>> is > >>>> > >>>>> the reason for getting this result? > >>>>> For the MD run I used the mdp file below: > >>>>> > >>>>> ; 7.3.2 Preprocessing > >>>>> > >>>>> ;define = ; defines to pass to the > preprocessor > >>>>> > >>>>> > >>>>> ; 7.3.3 Run Control > >>>>> > >>>>> integrator = md ; md integrator > >>>>> > >>>>> tinit = 0 ; [ps] starting time > for > >>>>> > >>>> run > >>>> > >>>>> > >>>>> dt = 0.002 ; [ps] time step for > >>>>> integration > >>>>> > >>>>> nsteps = 100000000 ; maximum number > of > >>>>> steps to integrate, 0.002 * 100000000 = 200000 ps > >>>>> > >>>>> comm_mode = Linear ; remove center of > mass > >>>>> translation > >>>>> > >>>>> nstcomm = 100 ; [steps] > frequency of > >>>>> mass motion removal > >>>>> > >>>>> ;comm_grps = Protein Non-Protein ; group(s) for > center > >>>>> of > >>>>> mass motion removal > >>>>> > >>>>> > >>>>> ; 7.3.8 Output Control > >>>>> > >>>>> nstxout = 0 ; [steps] freq to write > coordinates > >>>>> > >>>> to > >>>> > >>>>> trajectory > >>>>> > >>>>> nstvout = 0 ; [steps] freq to write > velocities > >>>>> to > >>>>> trajectory > >>>>> > >>>>> nstfout = 0 ; [steps] freq to write forces to > >>>>> trajectory > >>>>> > >>>>> nstlog = 1000 ; [steps] freq to write > >>>>> energies > >>>>> to log file > >>>>> > >>>>> nstenergy = 1000 ; [steps] freq to write > >>>>> energies > >>>>> to energy file > >>>>> > >>>>> nstxtcout = 1000 ; [steps] freq to write > >>>>> coordinates to xtc trajectory > >>>>> > >>>>> xtc_precision = 1000 ; [real] precision to write > xtc > >>>>> trajectory > >>>>> > >>>>> xtc_grps = System ; group(s) to write to xtc > >>>>> trajectory > >>>>> > >>>>> energygrps = System ; group(s) to write to energy > >>>>> > >>>> file > >>>> > >>>>> > >>>>> cutoff-scheme = verlet > >>>>> > >>>>> ; 7.3.9 Neighbor Searching > >>>>> > >>>>> nstlist = 20 ; [steps] freq to update > >>>>> > >>>> neighbor > >>>> > >>>>> list > >>>>> > >>>>> ns_type = grid ; method of updating neighbor > >>>>> > >>>> list > >>>> > >>>>> > >>>>> pbc = xyz ; periodic boundary > conditions > >>>>> in > >>>>> all directions > >>>>> > >>>>> rlist = 0.8 ; [nm] cut-off distance for > the > >>>>> short-range neighbor list > >>>>> > >>>>> > >>>>> ; 7.3.10 Electrostatics > >>>>> > >>>>> coulombtype = PME ; Particle-Mesh Ewald > >>>>> > >>>> electrostatics > >>>> > >>>>> > >>>>> rcoulomb = 1.2 ; [nm] distance for Coulomb > >>>>> > >>>> cut-off > >>>> > >>>>> > >>>>> > >>>>> ; 7.3.11 VdW > >>>>> > >>>>> vdwtype = cut-off ; twin-range cut-off with > rlist > >>>>> where rvdw >= rlist > >>>>> > >>>>> vdw-modifier = potential-switch > >>>>> > >>>>> rvdw-switch = 1.1 > >>>>> > >>>>> rvdw = 1.2 ; [nm] distance for LJ > cut-off > >>>>> > >>>>> DispCorr = EnerPres ; apply long range dispersion > >>>>> corrections > >>>>> > >>>>> > >>>>> ; 7.3.13 Ewald > >>>>> > >>>>> fourierspacing = 0.12 ; [nm] grid spacing for FFT > grid > >>>>> when using PME > >>>>> > >>>>> pme_order = 4 ; interpolation order for > PME, 4 > >>>>> > >>>> = > >>>> > >>>>> cubic > >>>>> > >>>>> ewald_rtol = 1e-6 ; relative strength of > >>>>> Ewald-shifted potential at rcoulomb > >>>>> > >>>>> ewald-rtol-lj = 0.001 > >>>>> > >>>>> lj-pme-comb-rule = Geometric > >>>>> > >>>>> ewald-geometry = 3d > >>>>> > >>>>> epsilon_surface = 0 > >>>>> > >>>>> > >>>>> ; 7.3.14 Temperature Coupling > >>>>> > >>>>> tcoupl = v-rescale ; temperature > >>>>> coupling with > >>>>> > >>>>> tc_grps = system ; groups to couple > seperately to > >>>>> temperature bath > >>>>> > >>>>> tau_t = 0.1 ; [ps] time > >>>>> constant > >>>>> for coupling > >>>>> > >>>>> ref_t = 303 ; [K] reference > >>>>> temperature for coupling > >>>>> > >>>>> > >>>>> ; 7.3.17 Velocity Generation > >>>>> > >>>>> gen_vel = no ; generate velocities > according > >>>>> to > >>>>> Maxwell distribution of temperature > >>>>> > >>>>> gen_temp = 303 ; [K] temperature for Maxwell > >>>>> distribution > >>>>> > >>>>> gen_seed = -1 ; [integer] used to > initialize > >>>>> random generator for random velocities > >>>>> > >>>>> > >>>>> ; 7.3.18 Bonds > >>>>> > >>>>> constraints = h-bonds > >>>>> > >>>>> constraint_algorithm = LINCS ; LINear Constraint Solver > >>>>> > >>>>> continuation = no ; no = apply constraints to > the > >>>>> start configuration > >>>>> > >>>>> lincs_order = 4 ; highest order in the > expansion > >>>>> > >>>> of > >>>> > >>>>> the contraint coupling matrix > >>>>> > >>>>> lincs_iter = 1 ; number of iterations to > >>>>> correct > >>>>> for rotational lengthening > >>>>> > >>>>> lincs_warnangle = 30 ; [degrees] maximum angle > that a > >>>>> bond can rotate before LINCS will complain > >>>>> > >>>>> Best regards, > >>>>> > >>>>> Mahsa > >>>>> -- > >>>>> 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. > >>>> > >>>> > >> -- > >> ================================================== > >> > >> 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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