Dear Justin, Seriously I want to remove my confusion. I just read your one paper " J.Physical Chemistry B 2010, 114, 1652-60" Where you have studied stability of Alzheimer. I don't want to ask about umbrella sampling used for the calculation of PMF.
But , before the calculation of PMF , you have obtained simple dissociation using your pulling protocol of gromacs with constant velocity simulation at three different velocities. I am surprised that you have followed the obvious protocol of minimization the nvt the npt and then 100ns md production. then you took final structure of 100ns and made new box for pulling and followed the same minimisation and npt for short time. After this you did pulling along only one direction (one reaction coordinate) . I am surprised that how such a smooth force/time data you have obtained for all the velocities (0.01,0.001,0.005) . I am asking because for my simple 12bp dsDNA or 22bp siRNA , I also have followed similar protocol and fixed one end (say 5') of first strand and pulling opposite end (5') of second strand along the helical direction of the system. Here, I am getting force/time (in the .xvg ) data which is qualitatively similar behaviour like yours i.e. initially increasing then reach to maximum and then decreasing almost becomes to zero value. But , In mine case during initial time of pulling force is also negative as well large fluctuation of force . But not such a smooth Variation of force/time like your in this paper. In your case, force is increasing like linearly in the initial and reaches the maximum and then start to decrease. There is no problem to clarify the peak of force (maximum force) in your pulling (above mentioned paper). While in our case its very difficult to clarify the peak force due to large fluctuation in value. Can you please tell me something about the reason. Its smoothness is now became headache for my calculation in all the case of pulling. Hoping your response. -- *With Best-Rakesh Kumar Mishra* * (RA)CSD SINP Kolkata, India* *E-mail - rakesh.mis...@saha.ac.in <rakesh.mis...@saha.ac.in> * *Phone n. +91 9473662491, +918777496532* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.