[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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