<br>Hello All,<br><div class="gmail_quote"><br>I am new user of gromacs and I need to calculate the binding free energy of a ligand and a protein. With the help of your short manual (<a href="http://www.dillgroup.ucsf.edu/group/wiki/index.php/Free_Energy:_Tutorial" target="_blank">http://www.dillgroup.ucsf.edu/group/wiki/index.php/Free_Energy:_Tutorial</a>) I maneged to run 10 ns MD for each lambda values 0, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9 and 1.0. I am stuck with the analysis part as I am having "pro.ene" for all lambda values and I encrypted this file using "gmxdump" programme of Gromacs. My query is what value of potential energy should I consider ie. Energy, Av Energy or Sum Energy and should I compute averages considering values for each lambda values?.. Please guide in this respect.<br>
<br>My another query is how to use TI method as all my "dVpot/dlambda" values are zero?<br><br> time: 2.00000e+00 step: 1000<br> Component <b> Energy</b> <b>Av. Energy</b> <b>Sum Energy</b><br>
Bond 2.89178e+03 7.86885e+06 2.98932e+06<br> Angle 4.33606e+03 9.27276e+06 4.40540e+06<br> Proper Dih. 1.85050e+03 2.99658e+06 1.89975e+06<br> Improper Dih. 1.38446e+03 2.41601e+06 1.36937e+06<br>
LJ-14 1.73760e+03 3.36469e+06 1.78548e+06<br> Coulomb-14 2.71578e+04 5.23907e+06 2.70781e+07<br> LJ (SR) 1.34540e+05 5.19285e+08 1.35127e+08<br> Disper. corr. -6.31178e+03 0.00000e+00 -6.31809e+06<br>
Coulomb (SR) -8.32042e+05 1.17824e+09 -8.34087e+08<br> Coul. recip. -1.27416e+05 6.36014e+06 -1.27604e+08<br> <b> Potential -7.91871e+05 5.23558e+08 -7.93354e+08</b><br> Kinetic En. 1.31454e+05 5.70385e+08 1.31956e+08<br>
Total Energy -6.60417e+05 6.61059e+08 -6.61399e+08<br> Temperature 2.99909e+02 2.96895e+03 3.01054e+05<br> Pressure (bar) -1.33618e+02 1.07622e+07 -1.15561e+05<br> <b>dVpot/dlambda 0.00000e+00 0.00000e+00 0.00000e+00</b><br>
dEkin/dlambda 0.00000e+00 0.00000e+00 0.00000e+00<br> dG/dl constr. 0.00000e+00 0.00000e+00 0.00000e+00<br> Cons. rmsd () 2.61465e-06 0.00000e+00 0.00000e+00<br> Cons.2 rmsd () 2.53555e-06 0.00000e+00 0.00000e+00<br>
Vir-XX 5.07625e+04 6.91791e+09 4.59584e+07<br> Vir-XY -4.54422e+02 3.26812e+09 -1.69837e+05<br> Vir-XZ -9.10682e+01 2.94598e+09 -1.51244e+05<br> Vir-YX -4.63023e+02 3.25550e+09 -1.61940e+05<br>
Vir-YY 4.16830e+04 5.96310e+09 4.59609e+07<br> Vir-YZ -2.26695e+03 2.57459e+09 -2.05005e+05<br> Vir-ZX -6.48123e+01 2.95810e+09 -1.52941e+05<br> Vir-ZY -2.16991e+03 2.57380e+09 -2.09076e+05<br>
Vir-ZZ 4.53636e+04 7.44707e+09 4.55326e+07<br> Pres-XX (bar) -4.41344e+02 2.78371e+07 -1.25950e+05<br> Pres-XY (bar) 8.47194e+00 1.35226e+07 1.22414e+04<br> Pres-XZ (bar) 2.71928e+00 1.14178e+07 7.83060e+03<br>
Pres-YX (bar) 9.01445e+00 1.34668e+07 1.17433e+04<br> Pres-YY (bar) 1.57316e+02 2.43191e+07 -1.19376e+05<br> Pres-YZ (bar) 1.28780e+02 1.06389e+07 1.06513e+04<br> Pres-ZX (bar) 1.06321e+00 1.14706e+07 7.93766e+03<br>
Pres-ZY (bar) 1.22659e+02 1.06387e+07 1.09080e+04<br> Pres-ZZ (bar) -1.16825e+02 2.95390e+07 -1.01356e+05<br> #Surf*SurfTen 2.03398e+02 2.10116e+09 1.72049e+05<br> Mu-X -7.79429e+02 6.48563e+06 -9.72717e+05<br>
Mu-Y 1.71887e+01 7.62611e+06 -1.80408e+05<br> Mu-Z -1.81198e+02 1.54752e+07 -3.62600e+05<br> T-Protein 3.16288e+02 2.42899e+04 3.06235e+05<br> T-Non-Protein 2.98703e+02 3.43288e+03 3.00672e+05<br>
<br><font color="#888888"><br>
<input type="hidden"><input type="hidden"><div></div>
</font></div><br>-- <br>Best Regards<br>SUNITA GUPTA<br><br>
<input id="gwProxy" type="hidden"><input onclick="jsCall();" id="jsProxy" type="hidden"><div id="refHTML"></div>