[gmx-users] (no subject)
gangotri dey
holyriver6 at gmail.com
Wed Aug 9 20:10:28 CEST 2017
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 <nedomacho at gmail.com> 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 <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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