[gmx-users] Running simulation differences

Kevin Boyd kevin.boyd at uconn.edu
Mon Dec 17 16:02:51 CET 2018


First, with those associated errors I wouldn't say that those differences
are significant.

More to your question, Gromacs simulations with default parameters are not
generally reproducible. See the last 2 points in this section of the
reference manaul:

That text also gets at your question of correctness - if you ran for long
enough (and depending on what you're trying to observe), the quantities
from multiple runs from the same tpr *should* converge to the same value.


On Mon, Dec 17, 2018 at 9:53 AM Gonzalez Fernandez, Cristina <
cristina.gonzalezfdez at unican.es> wrote:

> Dear Gromacs users,
> I have tried to run twice the same simulation (same .tpr input file) in
> the same workstation, but the results I obtain significantly differ, for
> example: (-276.96 ± 40.7  kj/mol) and (-257.25  ± 35.86 kj/mol). Are these
> differences normal?
> As these results are different, how do I know which one is the valid?
> Thank you in advance,
> C.
> --
> Gromacs Users mailing list
> * Please search the archive at
> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.gromacs.org%2FSupport%2FMailing_Lists%2FGMX-Users_List&amp;data=02%7C01%7Ckevin.boyd%40uconn.edu%7C6704e463dbee4f3e07c208d6642f737f%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C1%7C636806552310125875&amp;sdata=Kga6a%2FnGEM5ub2hn2VENdLyGdMaXJPd4rBeoALC1C1s%3D&amp;reserved=0
> before posting!
> * Can't post? Read
> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.gromacs.org%2FSupport%2FMailing_Lists&amp;data=02%7C01%7Ckevin.boyd%40uconn.edu%7C6704e463dbee4f3e07c208d6642f737f%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C1%7C636806552310135879&amp;sdata=So9iGDmwEqrUXXP5a6RzR2ABxCVasdknXnRpZa7n6zI%3D&amp;reserved=0
> * For (un)subscribe requests visit
> https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmaillist.sys.kth.se%2Fmailman%2Flistinfo%2Fgromacs.org_gmx-users&amp;data=02%7C01%7Ckevin.boyd%40uconn.edu%7C6704e463dbee4f3e07c208d6642f737f%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C1%7C636806552310135879&amp;sdata=cnxBml6P6U4jTslZjerxZTfV4OFsQsG%2BQBvW8XoBhmM%3D&amp;reserved=0
> or send a mail to gmx-users-request at gromacs.org.

More information about the gromacs.org_gmx-users mailing list