najwa drici wrote: > > I made a MD simulation of solvated protein and i have the out put > file md.log , I took the part of " R M S - F L U C T U A T I O N S " > > > in order to calculating the ratio R = Δ E_tot /Δ E_kin who should be > less than 0.05 > > R = Δ E_tot /Δ E_kin = 3.33405e+002/8.21064e+001 = 4.0606
This looks to much, but you should probably verify that your simulation is in equilibrium first. Please put further questions on the mailing list. > > > my questionsa are: > > > is R=4.0606 a percentage ? i.e can i write R= 0.040606 ??? > > is my simulation is accurate ? > > > this is my md.log file > <====== ############################### ==> > <==== R M S - F L U C T U A T I O N S ====> > <== ############################### ======> > Energies (kJ/mol) > G96Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14 > 2.53814e+001 1.57197e+001 1.20353e+001 1.13133e+001 3.16586e+001 > LJ (SR) Coulomb (SR) Coulomb (LR) > Potential Kinetic En. > 2.54693e+002 4.29057e+002 3.23823e+002 3.41410e+002 8.21064e+001 > Total Energy Temperature Pressure (bar) > 3.33405e+002 2.27536e+000 3.26751e+002 > Total Virial (kJ/mol) > 6.61328e+002 4.23233e+002 4.20276e+002 > 4.23314e+002 6.56348e+002 4.19655e+002 > 4.19582e+002 4.18954e+002 6.49220e+002 > Pressure (bar) > 4.91246e+002 3.17484e+002 3.15086e+002 > 3.17539e+002 4.88127e+002 3.15631e+002 > 3.14572e+002 3.15128e+002 4.82007e+002 > Total Dipole (Debye) > 2.81842e+001 3.19246e+001 2.69345e+001 > T-Protein T-Non-Protein > 1.34141e+001 2.30678e+000 > > thank you > > > > > ------------------------------------------------------------------------ > Téléchargez le nouveau Windows Live Messenger ! Téléchargez Messenger, > c'est gratuit ! <http://get.live.com/messenger/overview> -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
