[gmx-users] Periodic molecules and minimum bonded cut-off

Andrew DeYoung adeyoung at andrew.cmu.edu
Thu Mar 8 02:55:58 CET 2012


I am running an NVT simulation involving a periodic molecule, which has
bonds that cross the boundaries of the simulation box.  So, I am using
periodic_molecules = yes in my .mdp file.  I am also using the following
cut-offs in my .mdp file:  

vdwtype = cut-off
coulombtype = PME
rlist = 1.65
rvdw = 1.65
rcoulomb = 1.65

grompp runs fine, with no errors.  However, mdrun gives me the following
note message at the beginning of the run (the simulation runs and finishes

NOTE: Periodic molecules: can not easily determine the required minimum
bonded cut-off, using half the non-bonded cut-off

If you have time, do you know if this message means that the non-bonded
cut-off (is this referring to rvdw and rcoulomb?) which is used in the
simulation is actually different than the cut-off I specify in the .mdp
file?  In other words, given the .mdp parameters above and the note message,
are these parameters being used?

vdwtype = cut-off
coulombtype = PME
rlist = 1.65
rvdw = 1.65
rcoulomb = 1.65

Or are these actually being used (one-half of what I specified) by the code?

vdwtype = cut-off
coulombtype = PME
rlist = 0.825
rvdw = 0.825
rcoulomb = 0.825

I have checked the .log file resulting from mdrun.  In the "Input
Parameters" section, it lists (among many others): 

vdwtype              = Cut-off
coulombtype          = PME
rlist                = 1.65
rlistlong            = 1.65
rvdw                 = 1.65
rcoulomb             = 1.65

whereas in the following section in the .log file, it says "Minimum cell
size due to bonded interactions: 0.825 nm."  Later in the .log file, it says
"Cut-off's:   NS: 1.65   Coulomb: 1.65   LJ: 1.65".  Near the end of the
.log file, it says:

The maximum allowed distance for charge groups involved in interactions is:
                 non-bonded interactions           1.650 nm
            two-body bonded interactions  (-rdd)   1.650 nm
          multi-body bonded interactions  (-rdd)   0.849 nm
  atoms separated by up to 5 constraints  (-rcon)  0.849 nm

My question is, why does it use 0.849 nm for the "multi-body bonded
interactions" and "atoms separated by up to 5 constraints," rather than
1.650 nm?  Is there any way that I can force these terms to be 1.650 nm
instead?  (Or should I?)  Also, if you have time, what is a multi-body
bonded interaction?  I cannot seem to find this in the manual.

Thank you so very much for your time!

Andrew DeYoung
Carnegie Mellon University

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