[gmx-users] Initial cell size is smaller than the cell size

[David van der Spoel]

On 13/09/16 17:51, Faust SHI wrote:
> Hi David,
>
> I tried to set periodic-molecules=yes and the simulation could run but only one step. There are warnings in output file that “
> WARNING: Listed nonbonded interaction between particles 191795 and 191792
> at distance 2.716 which is larger than the table limit 2.500 nm.
>
> This is likely either a 1,4 interaction, or a listed interaction inside
> a smaller molecule you are decoupling during a free energy calculation.
> Since interactions at distances beyond the table cannot be computed,
> they are skipped until they are inside the table limit again. You will
> only see this message once, even if it occurs for several interactions.
>
> And several warnings between other atoms are found. Besides there is also information about missing interactions and fatal error, which is “
>
> A list of missing interactions:
>                 Bond of   1600 missing     67
>                Angle of   1800 missing    113
>          Proper Dih. of   1400 missing     96
>                LJ-14 of   1400 missing     62
>
> Molecule type 'SDS'
> the first 10 missing interactions, except for exclusions:
>                 Bond atoms    1    2           global191701191702
>                 Bond atoms    1    3           global191701191703
>                 Bond atoms    1    4           global191701191704
>          Proper Dih. atoms    1    5    6    7 global191701191705191706191707
>                Angle atoms    2    1    3      global191702191701191703
>                Angle atoms    2    1    4      global191702191701191704
>                Angle atoms    3    1    4      global191703191701191704
>                 Bond atoms    5    1           global191705191701
>                Angle atoms    5    1    2      global191705191701191702
>                Angle atoms    5    1    3      global191705191701191703
>                 Bond atoms    1    2           global191718191719
>                 Bond atoms    1    3           global191735191737
>                 Bond atoms    1    4           global191752191755
>                 Bond atoms    1    2           global191769191770
>                 Bond atoms    1    2           global191786191787
>          Proper Dih. atoms   13   14   15   16 global191968191969191970191971
>          Proper Dih. atoms   13   14   15   16 global192138192139192140192141
>          Proper Dih. atoms   13   14   15   16 global192308192309192310192311
>          Proper Dih. atoms   13   14   15   16 global192478192479192480192481
>          Proper Dih. atoms   13   14   15   16 global192648192649192650192651
>          Proper Dih. atoms   13   14   15   16 global192818192819192820192821
>          Proper Dih. atoms   13   14   15   16 global192988192989192990192991
>          Proper Dih. atoms   13   14   15   16 global193158193159193160193161
>          Proper Dih. atoms   13   14   15   16 global193328193329193330193331
>
> -------------------------------------------------------
> Program gmx mdrun, VERSION 5.1.2
> Source code file: /share/apps/home_2/yshi/GROMACS2016/gromacs-5.1.2/src/gromacs/domdec/domdec_topology.cpp, line: 435
>
> Fatal error:
> 338 of the 6200 bonded interactions could not be calculated because some atoms involved moved further apart than the multi-body cut-off distance (0.75 nm) or the two-body cut-off distance (1.5 nm), see option -rdd, for pairs and tabulated bonds also see option -ddcheck
>
> And the initial state information in log file which is “
>
> There are: 193500 Atoms
> Atom distribution over 24 domains: av 8062 stddev 3613 min 1921 max 11896
>
> Constraining the starting coordinates (step 0)
>
> Constraining the coordinates at t0-dt (step 0)
> Large VCM(group SOL):      0.00001,     -0.00001,      0.00001, Temp-cm:  2.23564e+37
> RMS relative constraint deviation after constraining: 0.00e+00
> Initial temperature: 2.72543e-06 K
>
> Started mdrun on rank 0 Mon Sep 12 20:49:26 2016
>            Step           Time         Lambda
>               0        0.00000        0.00000
>
>
> Not all bonded interactions have been properly assigned to the domain decomposition cells
>
> The initial temperature is almost 0. Is is reasonable?
Irrelevant.

One possibility may be that the order of atoms in your topology does not 
match your gro file, but for sure if you have bonds between atoms at 2.7 
nm something is fishy. Just highlight those atoms in VMD to check it.

>
> I also use VMD to see what happened and found some atoms in my surfactant ran through the box and the bonds were super long. Does it mean my molecules are actually not periodic?
>
> Thanks for your patience!
>
> Yours sincerely,
> Faust
> 在 2016年9月12日，下午1:15，gromacs.org_gmx-users-request at maillist.sys.kth.se<mailto:gromacs.org_gmx-users-request at maillist.sys.kth.se> 写道：
>
> I suspect your surfactants are cut in two by periodic boundary
> conditions. There must be more information in the log file about the
> distance of bonded interactions which are strange. Normally a bond is
> 0.15 nm but in your case it seems like yo have bonds that are 11 nm.
> If your molecules are periodic you need to set the appropriate option in
> the mdp file.
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
> spoel at xray.bmc.uu.se<mailto:spoel at xray.bmc.uu.se>    http://folding.bmc.uu.se
>


-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se