Dear Alex and Mark, Thank you for your kind reply.
To begin with I am a Postdoc but with expertise is in DFT. It is my first venture into force field MD calculations. Hence, I am struggling. My group and the boss has similar expertise. So we have turned to public forums to ask questions. My system is a brick floating in the water as you have correctly identified. My system is a periodic MnO2 surface. It has triclinic crystal system. I want it to be solvated in all 3 directions but within the boundary of the unit cell. This means that I do not want any water molecule between the surface and its continuous periodic image. I want the water to be maximum in the z-direction. I am using the 5.0.4 version. I tried gmx_mpi insert_molecule and then -nmol and -ip option. But this still generates a structure with water molecules beyond the desired x and y plane. I am not sure how can I get this done as desired. If the question and the problem are not very clear, please let me know. I will try to reframe my words. Looking forward to a healthy discussion. Thank you G. *Thank you* *Gangotri Dey* Postdoctoral Associate Rutgers University New Brunswick Chemistry and Chemical Biology 174 Frelinghuysen Road, Piscataway, NJ 08854 Phone: +16092162254 On Mon, Aug 7, 2017 at 8:06 PM, Alex <[email protected]> wrote: > > I did not quite understand your comment. >>> >>> However, I am trying my best to answer it. >>> I have a surface MnO2 model. I have solvated the structure in all 3 >>> directions. After that, I minimize it and run NVT simulation with the >>> parameters as mentioned. However, I see that there is a deformation of >>> the >>> surface and it does not remain a flat surface. Instead, it curls like a >>> ribbon. This should not be the case. Hence, I am wondering what are the >>> factors that can lead to this deformation? Are the parameters in the NVT >>> simulation good enough or else there is a problem that I cannot see. >>> >>> G >>> >>> There are a few points to be made... > 1. The shape of your system, which is "solvated in all 3 directions" is > very unclear. Is this a brick floating in water? > 2. Please do not solvate anything until you have established that your > "surface" is happy in vacuum. > 3. If you have bending as a whole, it could be indicative of large > internal strains, in which case NVT is probably a poor option. When you say > you have "a surface MnO2 model," is it something like this? > https://upload.wikimedia.org/wikipedia/commons/8/81/Manganes > e-dioxide-from-xtal-sheet-3D-balls.png > 4. This community is mostly focused on biomolecular simulations and noone > will be able to verify your parameterization of a solid crystal. Here is > the rule of thumb though: If something bends when it shouldn't bend, your > model is bad, which really has nothing to do with Gromacs. > 5. If you are a student and points 1-4 aren't something your doctoral > advisor already mentioned, maybe you should find another advisor. > > Alex > > > Hi, >>>> >>>> Are you trying to implement a model that you know is capable of produce >>>> a >>>> surface that does not deform in unexpected ways? >>>> >>>> Mark >>>> >>>> On Mon, 7 Aug 2017 16:35 gangotri dey <[email protected]> wrote: >>>> >>>> Dear all, >>>>> >>>>> I am trying to equilibrate a MnO2 surface (not cluster but periodic). I >>>>> have solvated the surface with water in all 3 directions. After the NVT >>>>> run, I see that the surface is deformed. I was wondering what else can >>>>> >>>> I >>> >>>> add in my nvt.mdp to not encounter this problem? >>>>> >>>>> I have mainly followed the examples in the forum for graphene/CNT >>>>> >>>> growth. >>> >>>> title = MnO2 in H2O NVT equilibration >>>>> ; Run parameters >>>>> integrator = md ; leap-frog integrator >>>>> nsteps = 50000 ; 2 * 500000 = 100 ps >>>>> dt = 0.002 ; 2 fs >>>>> ; Output control >>>>> nstxout = 50 ; save coordinates every 0.10 ps >>>>> nstvout = 50 ; save velocities every 0.10 ps >>>>> nstenergy = 50 ; save energies every 0.10 ps >>>>> nstlog = 50 ; update log file every 0.10 ps >>>>> ; Bond parameters >>>>> continuation = no ; first dynamics run >>>>> constraint_algorithm = lincs ; holonomic constraints >>>>> constraints = none ; all bonds (even heavy atom-H >>>>> bonds) constrained >>>>> lincs_iter = 1 ; accuracy of LINCS >>>>> lincs_order = 4 ; also related to accuracy >>>>> ; Neighborsearching >>>>> cutoff-scheme = Verlet >>>>> ns_type = grid ; search neighboring grid cells >>>>> nstlist = 10 ; 20 fs, largely irrelevant >>>>> >>>> with >>> >>>> Verlet >>>>> rcoulomb = 1.0 ; short-range electrostatic >>>>> >>>> cutoff >>>> >>>>> (in nm) >>>>> rvdw = 1.0 ; 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 = SOL MnO ; three coupling groups - more accurate >>>>> tau_t = 0.1 0.1 ; time constant, in ps >>>>> ref_t = 300 300 ; 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 >>>>> periodic-molecules = yes >>>>> ; Dispersion correction >>>>> DispCorr = EnerPres ; account for cut-off vdW scheme >>>>> ; Velocity generation >>>>> gen_vel = yes ; assign velocities from Maxwell >>>>> distribution >>>>> gen_temp = 300 ; temperature for Maxwell distribution >>>>> gen_seed = 188888 ; generate a random seed >>>>> >>>>> >>>>> *Thank you* >>>>> >>>>> *Gangotri Dey* >>>>> Postdoctoral Associate >>>>> Rutgers University New Brunswick >>>>> Chemistry and Chemical Biology >>>>> 174 Frelinghuysen Road, Piscataway, NJ 08854 >>>>> Phone: +16092162254 >>>>> -- >>>>> 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]. >>>> >>>> -- >>> 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]. > -- 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].
