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

[Justin A. Lemkul]

Andrew DeYoung wrote:
> Hi,
> 
> 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
> fine):
> 
> ---
> 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.
> 

All of these messages have to do with the configuration of the DD cells.  The 
details are explained in the Gromacs 4 paper:

http://pubs.acs.org/doi/abs/10.1021/ct700301q

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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