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

Jernej Zidar jernej.zidar at gmail.com
Wed Sep 4 03:56:34 CEST 2013

> 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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