[gmx-users] Fat-bottom restrain

[Alex]

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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>