[gmx-users] (no subject)
Alex
nedomacho at gmail.com
Tue Aug 8 02:06:16 CEST 2017
>> 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/Manganese-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 <holyriver6 at gmail.com> 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
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