Maybe this is better https://imgur.com/hLFbjS8 <https://imgur.com/hLFbjS8>
> On 18 Jul 2016, at 17:40, gozde ergin <gozdeeer...@gmail.com> wrote: > > Thanks Justin, > > Here is the plot for the average of 1ns chunks of time (with error) > > https://imgur.com/FPmxysO <https://imgur.com/FPmxysO> > > It is hard to tell. > > >> On 18 Jul 2016, at 16:18, Justin Lemkul <jalem...@vt.edu >> <mailto:jalem...@vt.edu>> wrote: >> >> >> >> On 7/18/16 10:16 AM, gozde ergin wrote: >>> Seems there is no systematic drift and trend but fluctuating is, please see >>> on >>> http://imgur.com/Vfs0wqw <http://imgur.com/Vfs0wqw> >>> <http://imgur.com/Vfs0wqw <http://imgur.com/Vfs0wqw>> >>> >> >> This is not what I suggested. The raw time series shows lots of noise. >> What happens when you plot the average of 1-ns chunks of time (with error >> bars), e.g. 0-1, 1-2, 2-3, etc? This helps you to determine if there are >> systematic changes. >> >>>> How did you decide that this division of time was appropriate? >>> >>> This is exactly my question how can I decide the simulation time is enough >>> or not. Also this surface tension value is not correct either. >>> It should be around 1000-1100 not 1244 bar nm. >>> >> >> Well, this could be any number of things: insufficient sampling, poor >> topology, system size, etc. >> >> -Justin >> >>> >>> On 18 Jul 2016, at 16:06, Justin Lemkul <jalem...@vt.edu >>> <mailto:jalem...@vt.edu>> wrote: >>>> >>>> >>>> >>>> On 7/18/16 6:07 AM, gozde ergin wrote: >>>>> Dear users, >>>>> >>>>> I am trying to estimate the surface tension of cis-pinonic covered water >>>>> surfaces. >>>>> Li. et al 2010 did the same thing and his simulation time was 2 ns. >>>>> On the other hand there are some other studies mentioned that simulation >>>>> time should be long around 200 ns because surface tension is difficult to >>>>> estimate accurately, since fluctuations are large and convergence is slow >>>>> (Engin et. al 2010). >>>>> >>>>> I would like to give a an example below. I simulated the system for 20 >>>>> ns. First 6 ns is for equilibration and last 14 ns sampling. >>>>> >>>> >>>> How did you decide that this division of time was appropriate? >>>> >>>>> For first 6 ns : >>>>> >>>>> Energy Average Err.Est. RMSD Tot-Drift >>>>> ------------------------------------------------------------------------------- >>>>> #Surf*SurfTen 1181.02 22 2327.09 32.8309 >>>>> (bar nm) >>>>> >>>>> For last 14 ns: >>>>> >>>>> Energy Average Err.Est. RMSD Tot-Drift >>>>> ------------------------------------------------------------------------------- >>>>> #Surf*SurfTen 1244.15 10 2339.36 -63.287 >>>>> (bar nm) >>>>> >>>>> RMSD is larger than Average value so i am confused how long should I run? >>>>> >>>> >>>> What happens if you plot your results in 1-ns chunks of time? Any >>>> systematic drift or trend? >>>> >>>> -Justin >>>> >>>> -- >>>> ================================================== >>>> >>>> Justin A. Lemkul, Ph.D. >>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow >>>> >>>> Department of Pharmaceutical Sciences >>>> School of Pharmacy >>>> Health Sciences Facility II, Room 629 >>>> University of Maryland, Baltimore >>>> 20 Penn St. >>>> Baltimore, MD 21201 >>>> >>>> jalem...@outerbanks.umaryland.edu >>>> <mailto:jalem...@outerbanks.umaryland.edu> | (410) 706-7441 >>>> http://mackerell.umaryland.edu/~jalemkul >>>> <http://mackerell.umaryland.edu/~jalemkul> >>>> >>>> ================================================== >>>> -- >>>> Gromacs Users mailing list >>>> >>>> * Please search the archive at >>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! >>>> >>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>> >>>> * For (un)subscribe requests visit >>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send >>>> a mail to gmx-users-requ...@gromacs.org. >>> >> >> -- >> ================================================== >> >> Justin A. Lemkul, Ph.D. >> Ruth L. Kirschstein NRSA Postdoctoral Fellow >> >> Department of Pharmaceutical Sciences >> School of Pharmacy >> Health Sciences Facility II, Room 629 >> University of Maryland, Baltimore >> 20 Penn St. >> Baltimore, MD 21201 >> >> jalem...@outerbanks.umaryland.edu <mailto:jalem...@outerbanks.umaryland.edu> >> | (410) 706-7441 >> http://mackerell.umaryland.edu/~jalemkul >> <http://mackerell.umaryland.edu/~jalemkul> >> >> ================================================== >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List >> <http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List> before posting! >> >> * Can't post? 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