[gmx-users] query on table potential

Mark Abraham Mark.Abraham at anu.edu.au
Fri Jun 8 05:16:48 CEST 2012

On 8/06/2012 1:09 PM, Sanku M wrote:
> Hi,
>   I am trying to use a table potential implementing 
> Weeks-Chandler-Anderson (WCA) interaction between a solute and all 
> atoms of a solvent like TIP3P water ( with nonzero interaction in the 
> Hydrogen atoms) . But, I am having a trouble in specifying energy 
> groups required for table potential.
> Here is the problem:
>  I have two atom types in water : OW and HW. and one atom type in 
> solute : POL
> Now, I want to use  two Table potentials with WCA interactions between 
> a) POL & HW and b) POL & OW
> So, I created two table potential files: table_POL_HW.xvg and 
> table_POL_OW.xvg
> and then
> in the .mdp file, I specified
> energygrps = POL OW HW
> energygrps_table = POL OW POL HW
> But, compiling the .mdp file using grompp ( version 4.5.4)  gives me 
> following error
> "Fatal error:
> atoms 33 and 34 in charge group 1 of molecule type 'SOL' are in 
> different energy groups"
> Clearly, using OW and HW as separate energy groups is causing the problem.
> So, I am looking for an option on how I can use the table potential 
> between solute and each atoms of solvent.

Energy groups can only be unions of complete charge groups. So your 
energy groups require that you split the solvent charge group. The 
solvent charge groups are defined in its [moleculetype]. Splitting will 
mean that you will get integration artefacts at the cut-off unless you 
use a proper long-ranged electrostatic method (i.e. an Ewald family method).

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120608/b1023b58/attachment.html>

More information about the gromacs.org_gmx-users mailing list