[gmx-users] Fluctuation properties

[David van der Spoel]

Den 2018-09-28 kl. 23:16, skrev Pelin S Bulutoglu:
> Dear Dr. Spoel,
> 
> 
> Thank you for your reply. Do you mean calculating fluctuation properties for different pieces of the energy file and calculating std deviation? I tried that but the std deviation changes depending on the length of the blocks that I use.
If they change a lot then your blocks may be too short or your 
trajectory not in equilibrium.
> 
> 
> Regards,
> 
> Pelin Su Bulutoglu
> 
> ________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of David van der Spoel <spoel at xray.bmc.uu.se>
> Sent: Friday, September 28, 2018 4:37:42 PM
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Fluctuation properties
> 
> Den 2018-09-28 kl. 21:18, skrev Pelin S Bulutoglu:
>> Dear Gromacs users,
>>
>>
>> How can I assess the uncertainty of the properties calculated with the -fluct_props option in gmx energy? Since these are fluctuation properties, I cannot make an error estimation such as block averaging. Any suggestion is appreciated.
>>
> You will have to do it manually for now by cutting your energy file in
> pieces (well, use the -b and -e options).
> 
>>
>> Regards,
>>
>>
>> Pelin Su Bulutoglu
>>
>> Graduate Research Assistant
>>
>> School of Chemical Engineering
>>
>> Purdue University
>>
> 
> 
> --
> David van der Spoel, Ph.D., Professor of Biology
> Head of Department, Cell & Molecular Biology, Uppsala University.
> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
> http://www.icm.uu.se
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-- 
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se