[gmx-users] Implicit solvent models in Gromacs ?

Marc Baaden baaden at smplinux.de
Wed Dec 12 14:11:53 CET 2001


Sorry, .. I first sent the reply to David only, not to the list ...

>>> David van der Spoel said:
 >> You have to make a user defined potential (using tables).
 >> You can then use V=1/r^2 for the Coulomb if you so wish, but check your
 >> units! People usually have this when r is in Angrstrom, so in the GROMACS
 >> case you need a factor 10 somewhere. Check the file table6-12.xvg in the
 >> top directory, that you have to modify, and then pass it to mdrun.

OK. That is fine.
BUT .. what format is that table file ? From the handbook page 166 I
would have expected 4 columns yi, Fi, Gi and Hi, but there are 7 of those ..


Also I wonder whether there is any example program/script, ..
which shows how table6-12.xvg is calculated (and even better
where I could just replace the epsilon-r by 1/r^2 to get what
I want ....)


Which is the actual part (function) stored in the table ?
E.g. if you have

               qi * qj
Vcoulomb = f * --------
               er * rij

I suppose the tabulated function would be
   
           f
y(x) = --------
        er * x

where x=rij

as qi and qj depend on the atom types of at i and j and cannot be included
in the table. Is that right ?

Am I also right that you actually have to store values only up to the
Cutoff you are going to use (eg the values in table6-12 go from 0 to
2 (nm), which should be more than enough).


What are the files table6-10.xvg, table6-11.xvg, table6-8.xvg and
table6-9.xvg ?


I also wonder wether there are any example ctab.xvg, rtab.xvg, .. files
for Gromacs 2.0. They seem to be of a different format (Gromacs complains
and says "Fatal error: Trying to read file ctab.xvg, but no colums = 7,
should be 5 "


Marc

-- 
 Dr. Marc Baaden - Laboratory of Molecular Biophysics, Oxford University
 mailto:baaden at smplinux.de  - ICQ# 11466242 -  http://www.marc-baaden.de
 FAX/Voice +49 697912 39550  -  Tel: +44 1865 275380  or  +33 609 843217



-- 
 Dr. Marc Baaden - Laboratory of Molecular Biophysics, Oxford University
 mailto:baaden at smplinux.de  - ICQ# 11466242 -  http://www.marc-baaden.de
 FAX/Voice +49 697912 39550  -  Tel: +44 1865 275380  or  +33 609 843217



-- 
 Dr. Marc Baaden - Laboratory of Molecular Biophysics, Oxford University
 mailto:baaden at smplinux.de  - ICQ# 11466242 -  http://www.marc-baaden.de
 FAX/Voice +49 697912 39550  -  Tel: +44 1865 275380  or  +33 609 843217





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