[gmx-users] free energy tutorial

[bharat v. adkar]

Dear GMX users,

i am trying 'relative hydration free energy of p-cresol wrt toluene' tutorial 
from http://md.chem.rug.nl/education/Free-Energy_Course/3.mutation-fe.html. i am using all the mdp files given on 
the site, the confout.gro from toluene/eq directory of the previous tutorial as starting structure for this simulation. 
and whatever relevant changes has to be made in top and gro have been made. then i performed the simulation for lamda 
values from zero to one with an interval of 0.4, so total of 26 simulations. but i am not getting the mentioned 
experimental value of ddG-hyd.

i got the following values in rmsd.xvg

        IN WATER                    IN VACUO
==========================   ============================
0    -61.874991   2.59103    0    -98.521845   8.80653
.04  -57.180709   1.73975    .04  -67.562344   0.237903
.08  -58.786951   0.266783   .08  -64.780817   1.23656
.12  -60.764221   0.300319   .12  -63.280561   1.14712
.16  -62.700774   0.313339   .16  -60.123999   0.926409
.20  -65.107642   1.26388    .20  -58.584394   0.103875
.24  -63.749578   0.384702   .24  -56.668703   1.02234
.28  -64.267572   1.22184    .28  -54.837984   0.0807904
.32  -61.524424   0.402878   .32  -53.550764   0.0760657
.36  -55.897929   0.314078   .36  -51.510805   0.0622261
.40  -49.084890   1.05137    .40  -49.736461   0.0627338
.44  -38.339801   1.39297    .44  -48.470839   0.0718284
.48  -29.613058   1.38755    .48  -46.842750   0.0740531
.52  -24.891702   1.04125    .52  -45.007666   0.0766915
.56  -25.435188   1.70549    .56  -43.939682   0.101024
.60  -25.180946   1.82089    .60  -41.844138   0.111544
.64  -28.395296   0.849711   .64  -41.250909   0.13644
.68  -29.672103   2.26016    .68  -41.182423   0.139366
.72  -34.441109   2.00941    .72  -41.747919   0.127424
.76  -39.148106   2.01051    .76  -44.426396   0.143008
.80  -49.360365   2.34239    .80  -44.381975   0.135462
.84  -57.031557   2.79298    .84  -45.564523   0.123685
.88  -64.059494   2.79089    .88  -46.074452   0.104784
.92  -78.668957   1.97957    .92  -46.678656   0.0993529
.96  -85.671014   1.92346    .96  -46.871521   0.0923201
1.0  -52.956186   1.26136    1.0  -47.183714   0.0934921


upon integration in xmgr, following are the dG values:
dG-wat = -50.6556 kJ.mol-1
dG-vac = -51.1109 kJ.mol-1

ddG-hyd = 0.455 kJ.mol-1

the experimental value mentioned on the site is -22.1 kJ.mol-1

Please help...

bharat