Hi Bob! Trjconv with fit-option will remove the COM motion of the droplet so that I actually see surface approaching the droplet whose COM is kept fixed. I think that the whole system is just centered always so that COM of the droplet stays fixed. The trajectory still includes translational motion in droplet velocities and g_traj gives temperature which corresponds to sum of thermal motion and translational motion. I suppose that mdrun -rerun will give the same solution for the new trajectory but I still have to test it tomorrow...
Janne > So, does g_traj really give you a trajectory that has the COM velocity > of the droplet removed? It looks like this is what you were trying to > do, but I just wanted to be clear on the outcome. > > If that is the case you can do an mdrun -rerun no-com-traj.trr. This > will feed your COM removed trajectory to mdrun and will recalculate > the energies (including temperature). > Bob > > On 2/22/07, Janne Hirvi <[EMAIL PROTECTED]> wrote: > > Hi! > > > > Still one check because g_traj even with com -option actually gives total > > temperature not the center of mass temperature as you agreed at the end of > > recent reply. So you mean that I should use g_traj to extract the center > of > > mass velocity (or translation energy) and calculate the contribution to > total > > temperature (or kinetic energy) with equation > > > > 0.5*m(total)*v(COM)^2=0.5*N(df)*k*T > > > > and just substract it to be able to calculate thermal motion temperature? > Is > > this the same procedure what is done when temperatures are written in .edr > > -file when acceleration is used together with temperature coupling while > > temperature given by g_energy is smaller than the one given by g_traj? > > > > Thanks for your time and help, > > > > Janne > > > > > > > Janne Hirvi wrote: > > > > Hello David and other gmx-experts! > > > > > > > > I havent yet been able to extract thermal motion contribution for > > > temperature > > > > (without translation) even I tested trjconv with fit (translation) > option > > > as > > > > you adviced. Actually, I was able to remove the center of mass > translation > > > of > > > > the droplet (tested with g_traj -ox) but however analyze still gives > the > > > center > > > > of mass velocity which contributes to temperature (g_traj with -ov and > > > -ot)? > > > > > > Maybe trjconv does not modify the center of mass velocity. > > > > > > What you can do is from your original trajectory calculate the center of > > > mass temperature with g_traj and subtract that from the normal T. You > > > may have to be careful with degrees of freedom. > > > > > > > > > > > I am wondering how thermal motion contribution for temperature is > extracted > > > by > > > > g_energy in case of acceleration combined with temperature coupling, > while > > > > g_traj seems to include also translational motion. At least g_traj > > > temperature > > > > is higher and almost equal to reference temperature + temperature > increase > > > due > > > > to translational energy(0.5*m(total)*v(COM)^2)). So, I think g_traj > > > temperature > > > > is calculated directly from the velocities > > > > (0.5*SUM(m(i)*v(i)^2)=0.5*N(df)*k*T), but are (1) these velocities > scaled > > > to > > > > remove the center of mass velocity to get temperature given by g_energy > or > > > is > > > > (2) translational energy contribution directly substracted from the > total > > > > kinetic energy? I tested the latter method and got pretty good > agreement, > > > but > > > > not perfect, between g_energy and g_traj temperatures but is it the > exact > > > > method? > > > > > > g_energy does not do any processing of data, just reading the energy > > > file and printing it. > > > g_traj calculates T using above equation. _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users 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
