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

Jernej Zidar jernej.zidar at gmail.com
Wed Sep 11 11:28:21 CEST 2013

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,

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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