[gmx-users] AdResS feature in gromacs
dududiniz94 at hotmail.com
Tue Jul 3 18:13:29 CEST 2018
Thank you for your reply
Exactly, VOTCA generated the thermoforce so it was able to perform an Adress simulation.
I've looked more carefully at the files generated by VOTCA and could not find a file that
might be this tablep.xvg. But I think that this problem is related to the
fact that my sistem have a protein. The system used for VOTCA to generate the thermoforce
contained only water molecules. I thought at first the the thermoforce generated for a system of
pure water could be transferred to other systems containing a solute. I don't know if this is correct.
I tried your suggestion and copied a 6-12 potential from gromacs/share/top/table6-12.xvg to a
tablep.xvg file and gmx mdrun returned:
AdResS full box therm force table in file tabletf.xvg extends to 7.100000:
should extend to at least for spherical adress13.569794 (=distance from center to furthermost point in box
which is related to the extension of my thermodynamic force table. This same table extension worked well for generating the
thermoforce with VOTCA. I don't know if the spheric atomistic region is attached
to some atom of the protein so it moves with the protein or if it is a static region, in which case the protein
would cross the transition region, what could explain the need for this tablep.xvg I think.
Please, if you could help I would really appreciate.
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
> 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.
More information about the gromacs.org_gmx-users