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

[Justin Lemkul]

On 9/11/13 5:28 AM, Jernej Zidar 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?
>

Run correctly in vacuo.

pbc = no
ns_type = simple
rvdw = 0
rcoulomb = 0
rlist = 0
nstlist = 0

-Justin

> 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.
>>
>
>
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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