[gmx-users] Fat-bottom restrain

[Alex]

Thanks Billy,

> If the flat bottom restraint energy is zero, then that means that the
> restraints aren't being applied, or your predefined distance is not being
> exceeded.  I doubt you would get binary zero values if it was the second
> option, so something is probably wrong with your syntax or your inclusion
> of the restraints

As far as I have inspected everything is fine with the syntax and
application of the restraints. Using similar way works fine in another
system. The only difference is that one (not working one) runs on GPU and
the other one (the working one) runs on CPU, and I am not sure if that
plays any role and if the flat-bottom restrain doesn't work on GPU!

>
> Cheers,
> Billy
>
> On Wed., 11 Sep. 2019, 5:20 pm Billy Williams-Noonan, <
> billy.williams-noonan at monash.edu> wrote:
>
> You may want to consider using smart-bottom restraints instead?
I haven't hear the smart-bottom one, would you please explain more? or
address me to a reference?
>
> Jokes aside, why does it matter if your molecules move into the next
> periodic image?
Just to avoid percolation across the period box.
>
> Cheers,
> Billy
Thank you,
Alex

On Wed, Sep 11, 2019 at 3:02 AM Alex <alexanderwien2k at gmail.com> wrote:

> Hi,
>
> Any comment, please?
>
> Thank you.
> Alex
>
> On Mon, Sep 9, 2019 at 10:22 PM Alex <alexanderwien2k at gmail.com> wrote:
>
>> Hi Mark,
>>
>> Thank you for your response.
>> Here are the part of options that gmx energy gives me out:
>>
>>   9  Coulomb-(SR)                        10  Coul.-recip.
>>  11  Flat-bottom-posres                  12  Potential
>>  13  Kinetic-En.     14  Total-Energy    15  Conserved-En
>>
>>
>> Energy                      Average   Err.Est.       RMSD  Tot-Drift
>>
>> -------------------------------------------------------------------------------
>> Coulomb (SR)             -8.4629e+06        150    5041.75   -840.379
>> (kJ/mol)
>> Coul. recip.                12689.7         12    109.811   -83.8453
>> (kJ/mol)
>> Flat-bottom posres                0          0          0          0
>> (kJ/mol)
>> Potential                -7.29781e+06        540    3208.53   -3702.71
>> (kJ/mol)
>> Kinetic En.              1.20527e+06        8.2    1912.61    -12.144
>> (kJ/mol)
>> Total Energy             -6.09255e+06        540     3942.5   -3714.84
>> (kJ/mol)
>> Conserved En.            -2.97263e+06     890000 1.81911e+06 6.30101e+06
>> (kJ/mol)
>>
>> As can be seen above the Flat-bottom posres energy is just zero during
>> the simulation; and even stiffening the force constant from 4184 KJ/(mol.
>> nm^2) to 4184000  KJ/(mol. nm^2) doesn't change anythings and the
>> Flat-bottom posres energy would remain absolutely zero!
>>
>> I rechecked everything and I don't see any problem with the way I have
>> set the flat-bottom restrain.
>> Any comment would be highly appreciated.
>>
>> Thank you,
>> Alex
>>
>>
>>
>> On Sat, Sep 7, 2019 at 10:47 AM Mark Abraham <mark.j.abraham at gmail.com>
>> wrote:
>>
>>> Hi,
>>>
>>> The total potential energy violating the restraints is reported, so you
>>> should see that there is an appropriate contribution there, and probably
>>> plan to stiffen the force constant.
>>>
>>> Mark
>>>
>>> On Fri., 6 Sep. 2019, 17:23 Alex, <alexanderwien2k at gmail.com> wrote:
>>>
>>> > Dear all,
>>> > Using the flat-bottom (K=4184 KJ/(mol. nm^2)) restrain I tried to have
>>> a
>>> > smaller cubic box as semi-preamble walls inside a bigger cubic box so
>>> that
>>> > all molecules except water would stay inside the smaller box during the
>>> > simulation, however, the wall doesn't work and the molecules are also
>>> out
>>> > of the smaller box in several replica's simulations each with 100 ns.
>>> > The only reason I can imagine is that the K=4184 KJ/(mol. nm^2 is
>>> probably
>>> > too low to keep the molecules inside the smaller box! I wonder if you
>>> know
>>> > any other potential reason? how can I find out the reason?
>>> >
>>> > Regards,
>>> > Alex
>>> > P.S. I am sure that I am using the flat-bottom restrain correctly as
>>> the
>>> > same approach worked for some other systems of mine previously.
>>> > --
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>>