Dear all, It is the first time that I use gromacs 4.04 to calculate PMF. I have some question needed to be clarified.
1. ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;; ; pull code for PMF pull = Unbrella ;unbrella,constraint pull_geometry = Distance ;distance ,direction,cylinder,position pull_dim = N N Y pull_group0 = DPPC pull_group1 = DEN pull_nstxout = 100 pull_nstfout = 100 pull_init1 = 3.8 pull_k1 = 1000 Is there any relationship between the steps for pull_nstxout and pull_nsfout. Must they be the same( e.g. 100, 100)? How to choose them? 2. It seems that there are only two output file: pullx.xvg and pullf.xvg. Is it right? are there other files for the input of g_wham? 3. What other thing I must take care of for calculation of PMF Thanks in advance. -- wende
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