[gmx-users] Implicit solvent

Marc Baaden baaden at smplinux.de
Fri Mar 8 12:35:12 CET 2002


sorry for the late reply, but I was away at a conference.

>> I am interested in finding solvation energies using an implicit solvent so
>> that I can use geometry optimization instead of MD (to save time). As far
>> as I can see, Gromacs contains several components needed to do this
>> (solvent accessible surface calculation, electrostatic solver), but cannot
>> yet perform the full calculation.
>> 1) Has anyone used Gromacs for implicit solvent calculations?
>> 2) If so, how did you do it?

I have done some simple runs using a modified sigmoidal dielectric function
(modified Hingerty-Lavery function) which looks like

                D - D  
                     0        2               -rS
  e   (r) = D - ------ [ (rS)  + 2 rS + 2 ] e
   eff            2

           D0 = 4 ; D = 80 ; S = 0.4
   ref eg  Rohs et al 1999, BPJ, 76, 2760-2768
       or  Arora et al 1997, JCC, 18, 1245-1252

This works via creating a user table that can be used via the -table option
to mdrun. The program for creating such a table came from Graham Smith, and
I modified it for the MHLF.

If anybody is interested in the table, I will gladly provide it, but I did
not want to increase the list traffic unnecessarily. Right now I have 
calculated it for up to 2 nm cutoffs.
(I meant to put it on the web, but I am too busy with other things right


 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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