原子受力（Atomic force）.doc

原子受力（Atomic force） If you are a novice, just want to simply look at the interaction force and energy changes it is recommended to use g_traj file extraction, g_energy extraction and g_hbond analysis of hydrogen bonding interaction energy, g_saltbr analysis, PMF can use g_wham, salt bridge; hydrophobic interaction and water bridge like direct analysis can not, need to use other software, you water bridge if you have trouble with the g_hbond calculation. Of course, you can also assist some, such as distance g_dist and other peak analysis, some articles are force, distance and energy to determine the peak value. [originality] enables VMD to display atomic force in GROMACS trajectories in real time Enable VMD to display atomic force in the GROMACS trajectory in real time Wen /Sobereva It is sometimes important to show the force of an atom, but it is a troublesome matter to realize. Since these two days need to use this function, so wrote a VMD TCL script, you can use arrows to display the force of the specified atom, and drag along with the progress bar, real-time updates, here to introduce. The current version of VMD does not read the force in the track and cannot be called directly inside, so you need to manually extract the force from the path and read it into the VMD. In this case, we have to analyze the serial number for the 977 atomic force, serial number by 0 starting. Heres a technique that combines gmxdump and grep to easily extract atomic force 977 from a.Trr file, although its slow, but very convenient: Gmxdump, -f, all.trr, |grep, F. 977 force.txt Rows containing f[977] are extracted. Force.txt reads as follows: F[, 977]={, 1.02676e+03, -1.37174e+03, 1.29441e+03} F[, 977]={, 5.54416e+01, 9.32820e+02, -7.47177e+02} F[, 977]={, 7.87461e+02, 7.43057e+02, -9.03874e+02} F[, 977]={, 1.52381e+02, -5.37775e+02, 1.38345e+02} F[, 977]={-6.90852e+02, -1.33539e+02, -9.30110e+02} ...... It should be noted that in order for each row to correspond to a frame structure,.Md