[gmx-users] Strange in PMF calculation (Shi Li)

[Justin Lemkul]

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On 11/22/16 7:29 PM, Shi Li wrote:

>> On 11/22/16 3:14 PM, Li, Shi wrote:
>>> Dear Gromacs users,
>>>
>>> I am doing some PMF simulations of 2 molecules in vacuum and my resulting
>>> profile has a strange look. I attached an eps files here, anyone can give
>>> me some suggestion on why there is fluctuation at longer distance?
>>>
>>
>> The mailing list does not accept attachments.  Upload an image to a file-sharing
>> service and provide the URL.
>>
>> -Justin
>>
>
> Thank you Justin,
>
> Here is the link to my eps file.
> https://www.dropbox.com/s/bc2ch1nujm0f825/syn.eps?dl=0 <https://www.dropbox.com/s/bc2ch1nujm0f825/syn.eps?dl=0>
>

Do you have sufficient sampling?  How is the overlap between the histograms? 
This could just be a small sampling defect.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

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