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

Faust SHI shi86 at wisc.edu
Tue Sep 13 17:51:42 CEST 2016

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?

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,
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

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