[gmx-users] AdResS feature in gromacs

Jan Henning Peters jan.henning.peters at fu-berlin.de
Tue Jul 3 16:50:51 CEST 2018

Hello Eduardo,

tablep.xvg contains the tabulated potential for 1-4 interactions, which 
are non-bonded interactions inside a molecule that usually only differ 
by the Lennard-Jones parameters sigma/epsilon (or C6/C12) but not the 
general shape of the potential. Since these should only occur in the 
fine-grained part, they should just be standard 6-12 Lennard-Jones 
potentials and you could just copy table.xvg (the 6-12 potential used 
for fine-grained non-bonded interactions) to tablep.xvg.

However, since you used VOTCA to generate the tabletf.xvg, it did 
successfully run AdResS simulations, so my guess is that you already 
have proper tablep.xvg files that were used in the tf generation (I 
would also assume that they are indeed identical to the table.xvg files 
used). Hence you could also copy a tablep.xvg file from one of the 
step_* subdirectories of your tf calculation run.



On 03/07/2018 15:24, Eduardo Diniz wrote:
> Hello everyone,
> I'm trying to run an simulation in gromacs with AdResS, where water is treated as fine grained in the region close to the protein and as coarse-grained in the farthest layers. I've already generated the tabulated potential for coarse-grained water with the VOTCA package and also the termodynamic force table with the same package. I generated the tpr file with no error and when I try to run mdrun the command complains about a missing file:
> System I/O error:
> Library file 'tablep.xvg' not found in current dir nor in the default
> directories.
> The following paths were searched:
> I have no idea what is this tablep.xvg file. There is no problem in finding the thermodynamic force (tabletf.xvg) nor the coarse-grained tabulated potential (table.xvg). I tested it by removing this files, the command shows a similar message but instead complaining about the table.xvg/tabletf.xvg missing file. I appreciate if anyone could help me.

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