[gmx-users] Re: MD vs. free energy simulations

[Mark Abraham]

Pressure coupling with a single molecule (i.e. in the gas phase)
doesn't sound workable to me.

Mark

On Wed, Sep 11, 2013 at 11:28 AM, Jernej Zidar <jernej.zidar at gmail.com> wrote:
> Dear Justin,
>
>   I followed your advice and started a gas-phase simulation. I removed the solvent and simulated only the polymer molecule but I ended up with this error:
> One of the box vectors has become shorter than twice the cut-off length or
> box_yy-|box_zy| or box_zz has become smaller than the cut-off.
>
>   What can I do to remedy this?
>
> Thanks in advance,
> Jernej
>
> On 4. sep. 2013, at 09:55, Jernej Zidar <jernej.zidar at gmail.com> wrote:
>
>>
>>> On 9/2/13 9:43 PM, Jernej Zidar wrote:
>>>> Dear Justin,
>>>>   I set the couple_intramol parameter to yes and rerun the free energy
>>>> simulations. mdrun was able to fully utilize all the cores in the
>>>> system but there's one issue. The free energy of solvation is vastly
>>>> different if the parameter is set to 'no' (DG=-408.10 +/- 8.69 kJ/mol)
>>>> or 'yes' (1890.14 +/- 15.52).
>>>>
>>>>   The behavior observed in the simulations is more consistent with the
>>>> latter number.
>>>>
>>>
>>> The latter number, of course, is not an actual final answer.  You have to do a
>>> corresponding gas-phase calculation to determine the real DG of solvation.
>>
>> I see. I'll do a gas-phase calculation as well.
>>
>>
>>>
>>>>   The manual states that 'yes' can be used can be "useful for
>>>> partitioning free-energies of relatively large molecules, where the
>>>> intra-molecular non-bonded interactions might lead to kinetically
>>>> trapped vacuum conformations. The 1-4 pair interactions are not turned
>>>> off."
>>>>
>>>>   My molecule has 161 atoms. How large is "relatively large" ?
>>>>
>>>
>>> I think a bigger factor is flexibility.  For a relatively rigid, conjugated
>>> system, it may not be a big issue.  Gut feeling?  Yes, I'd say that something
>>> with 161 atoms is relatively large.
>>>
>>
>> The polymer molecules is indeed very flexible.
>>
>
>
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