[gmx-users] Query regarding FEP

sunita gupta sunita.bio at gmail.com
Mon Feb 22 13:42:37 CET 2010

Hello All,

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 (
http://www.dillgroup.ucsf.edu/group/wiki/index.php/Free_Energy:_Tutorial) 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.

My another query is how to use TI method as all my "dVpot/dlambda" values
are zero?

        time:   2.00000e+00         step:          1000
               Component       * Energy*    *Av. Energy*    *Sum Energy*
                    Bond   2.89178e+03   7.86885e+06   2.98932e+06
                   Angle   4.33606e+03   9.27276e+06   4.40540e+06
             Proper Dih.   1.85050e+03   2.99658e+06   1.89975e+06
           Improper Dih.   1.38446e+03   2.41601e+06   1.36937e+06
                   LJ-14   1.73760e+03   3.36469e+06   1.78548e+06
              Coulomb-14   2.71578e+04   5.23907e+06   2.70781e+07
                 LJ (SR)   1.34540e+05   5.19285e+08   1.35127e+08
           Disper. corr.  -6.31178e+03   0.00000e+00  -6.31809e+06
            Coulomb (SR)  -8.32042e+05   1.17824e+09  -8.34087e+08
            Coul. recip.  -1.27416e+05   6.36014e+06  -1.27604e+08
              * Potential  -7.91871e+05   5.23558e+08  -7.93354e+08*
             Kinetic En.   1.31454e+05   5.70385e+08   1.31956e+08
            Total Energy  -6.60417e+05   6.61059e+08  -6.61399e+08
             Temperature   2.99909e+02   2.96895e+03   3.01054e+05
          Pressure (bar)  -1.33618e+02   1.07622e+07  -1.15561e+05
           *dVpot/dlambda   0.00000e+00   0.00000e+00   0.00000e+00*
           dEkin/dlambda   0.00000e+00   0.00000e+00   0.00000e+00
           dG/dl constr.   0.00000e+00   0.00000e+00   0.00000e+00
           Cons. rmsd ()   2.61465e-06   0.00000e+00   0.00000e+00
          Cons.2 rmsd ()   2.53555e-06   0.00000e+00   0.00000e+00
                  Vir-XX   5.07625e+04   6.91791e+09   4.59584e+07
                  Vir-XY  -4.54422e+02   3.26812e+09  -1.69837e+05
                  Vir-XZ  -9.10682e+01   2.94598e+09  -1.51244e+05
                  Vir-YX  -4.63023e+02   3.25550e+09  -1.61940e+05
                  Vir-YY   4.16830e+04   5.96310e+09   4.59609e+07
                  Vir-YZ  -2.26695e+03   2.57459e+09  -2.05005e+05
                  Vir-ZX  -6.48123e+01   2.95810e+09  -1.52941e+05
                  Vir-ZY  -2.16991e+03   2.57380e+09  -2.09076e+05
                  Vir-ZZ   4.53636e+04   7.44707e+09   4.55326e+07
           Pres-XX (bar)  -4.41344e+02   2.78371e+07  -1.25950e+05
           Pres-XY (bar)   8.47194e+00   1.35226e+07   1.22414e+04
           Pres-XZ (bar)   2.71928e+00   1.14178e+07   7.83060e+03
           Pres-YX (bar)   9.01445e+00   1.34668e+07   1.17433e+04
           Pres-YY (bar)   1.57316e+02   2.43191e+07  -1.19376e+05
           Pres-YZ (bar)   1.28780e+02   1.06389e+07   1.06513e+04
           Pres-ZX (bar)   1.06321e+00   1.14706e+07   7.93766e+03
           Pres-ZY (bar)   1.22659e+02   1.06387e+07   1.09080e+04
           Pres-ZZ (bar)  -1.16825e+02   2.95390e+07  -1.01356e+05
           #Surf*SurfTen   2.03398e+02   2.10116e+09   1.72049e+05
                    Mu-X  -7.79429e+02   6.48563e+06  -9.72717e+05
                    Mu-Y   1.71887e+01   7.62611e+06  -1.80408e+05
                    Mu-Z  -1.81198e+02   1.54752e+07  -3.62600e+05
               T-Protein   3.16288e+02   2.42899e+04   3.06235e+05
           T-Non-Protein   2.98703e+02   3.43288e+03   3.00672e+05

Best Regards
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