[gmx-users] Water molecule starting at atom 18511 can not be settled

[Alexander Alexander]

Dear Justin,

Thanks for the explanation.
Defiantly it is something with the epsilon, as for epsilon=17.0 not only
minimisation but also a 5 ns NVT calculation afterwards also is running
fine and it is in the very end steps now. But for epsilon = 64.65 it
crashes immediately
Please find the input files via below links.

https://drive.google.com/open?id=0B_CbyhnbKqQDZlpiMG8zU29BM2c

Cheers,
Alex

On Sat, Apr 16, 2016 at 7:49 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 4/16/16 1:44 PM, Alexander Alexander wrote:
>
>> Dear Christopher,
>>
>> If it is not a default, I have not applied any "SETTLE" in my calculation
>> as far as I know. Here is the .mdp file of my minimisation. Also the
>>
>
> SETTLE is on by default unless using -DFLEXIBLE, as defined in all water
> topologies.  Water models present in GROMACS are all intended to be rigid
> unless the user specifies otherwise.
>
> "define = -DFLEXIBLE" did not help.
>>
>>
> This suggests a problem with the force field.  The value you have set for
> epsilon is massive, several orders of magnitude larger than normal values.
> Likely the attraction between the Ni and OW is so large that it draws water
> molecules very close together, to the point that they are compressed into
> repulsive regions with each other.
>
> Providing a tarball of all your inputs (force field, coordinates,
> topologies uploaded to a file-sharing service and URL sent to the mailing
> list) would be helpful in diagnosing the problem and testing this idea.
>
> -Justin
>
>
> -----------------------------------
>> define = -DFLEXIBLE
>> integrator = steep
>> ;integrator = cg
>> ;integrator = l-bfgs
>> emtol = 10
>> emstep = 0.0001
>> nsteps = 100000000
>> nstlog = 1
>> nstenergy = 1
>> nstlist = 10
>> ns_type = grid
>> coulombtype = PME
>> rcoulomb = 1.26
>> vdwtype = cutoff
>> rvdw = 1.26
>> pme_order = 4
>> optimize_fft = yes
>> ;constraints = all-bonds
>> ;constraint_algorithm = LINCS
>> cutoff-scheme = Verlet
>> ;rlist = Cut-off distance for the short-range neighbor list.
>> pbc = xyz
>> ------------------------
>> Cheers,
>> Alex
>>
>>
>> On Sat, Apr 16, 2016 at 7:02 PM, Christopher Neale <
>> chris.neale at alum.utoronto.ca> wrote:
>>
>> Then don't use settle for your minimization?
>>> (mdp option define = -DFLEXIBLE for most water models)
>>>
>>> You can always turn it on again and run another EM after whatever
>>> problematic configurational feature has relaxed.
>>>
>>> ________________________________________
>>> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
>>> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of
>>> Alexander
>>> Alexander <alexanderwien2k at gmail.com>
>>> Sent: 16 April 2016 11:57
>>> To: gmx-users at gromacs.org
>>> Subject: Re: [gmx-users] Water molecule starting at atom 18511 can not be
>>>       settled
>>>
>>> Dear Mark,
>>>
>>> Thanks for your response.
>>> If I understood your statement correctly, I would say these numbers used
>>> here for the epsilon and sigma are not arbitrary but they come from some
>>> well quantum calculations (DFT) of water on this surface, actually,
>>> adsorption energy and optimized geometry of water on the surface were
>>> used
>>> in Lennard-Jones potentials to get sigma and epsilon, this means it is a
>>> sound model physics.
>>>
>>> Cheers,
>>>
>>> Alex
>>>
>>>
>>> On Sat, Apr 16, 2016 at 5:01 PM, Mark Abraham <mark.j.abraham at gmail.com>
>>> wrote:
>>>
>>> Hi,
>>>>
>>>> You will always need a sound model physics and a starting configuration
>>>> that is close enough to consistent with that. Which aspect do you think
>>>>
>>> is
>>>
>>>> wrong?
>>>>
>>>> Mark
>>>>
>>>> On Sat, Apr 16, 2016 at 3:58 PM Alexander Alexander <
>>>> alexanderwien2k at gmail.com> wrote:
>>>>
>>>> Dear Gromacs user,
>>>>>
>>>>> The minimisation (steepest descent) of water on surfaces of a nickel
>>>>> intermetallic compounds works fine if epsilon in the nonbond_params
>>>>>
>>>> below
>>>
>>>> is 17.0 (harvested from LJ(10-4)) but it will crash immediately if
>>>>>
>>>> epsilon
>>>>
>>>>> is elevated to 64.65 (harvested from LJ(12-6) or LJ(9-6)) with settling
>>>>> problem of one water molecule.
>>>>>
>>>>> [ nonbond_params ]
>>>>> ;     ai       aj    funct     sigma(nm)      epsilon (kj/mol)
>>>>>        Ni     OW     1          0.2072             64.65
>>>>>
>>>>> The settling problem of the molecule has been already discussed many
>>>>>
>>>> times
>>>>
>>>>> in mailing list but no helpful solution has been proposed yet.
>>>>> So any solution would be highly appreciated.
>>>>>
>>>>> Cheers,
>>>>> Alex
>>>>> --
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> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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