Many thanks Justin A. Lemkul wrote: > > > Gavin Melaugh wrote: >> Hi Justin >> >> I am not using periodic boundary conditions for the simulations. I may >> have sorted it out now. I was generating velocities in the umbrella.mdp >> file, I have since set gen_vel = no, and the histogram has the correct >> shape (should this make a difference?) >> > > If you generate velocities without doing equilibration, then your > system may not be at equilibrium and thus you are doing inaccurate > sampling. Thus, if your system gets kicked in the wrong direction, > the umbrella potential may have to fight to pull the desired group > back to where it thinks it should be, might be overcompensating, etc. > > -Justin > >> Cheers >> >> Gavin >> >> Justin A. Lemkul wrote: >>> Have you watched the trajectory? That will show you what your pull >>> group is doing. Is this a periodicity effect? It should be fairly >>> obvious iff the sign of dX, etc flip-flops in the pullx.xvg file. >>> >>> -Justin >>> >>> Gavin Melaugh wrote: >>>> Thanks Chris and Justin >>>> >>>> I do get the output I want from grompp(below). The distance of >>>> 5.507 nm >>>> is the distance that I want to start with and I assume it is therefore >>>> the equilibrium distance for the harmonic potential. The COM distances >>>> from the simulations fluctuate around this value which is what I want, >>>> although my histogram is the wrong shape. >>>> >>>> Pull group natoms pbc atom distance at start reference at t=0 >>>> 0 84 42 >>>> 1 84 126 >>>> 5.507 5.507 >>>> >>>> Cheers >>>> >>>> Gavin >>>> >>>> chris.ne...@utoronto.ca wrote: >>>>> I missed that pull_start = yes, sorry. So Gavin, your run should have >>>>> stayed around the starting position. Make the histogram directly and >>>>> you should get a better idea. >>>>> >>>>> Chris. >>>>> >>>>> -- original message -- >>>>> >>>>> >>>>> To clarify, the tutorial sets "pull_init1 = 0" because it is used in >>>>> conjunction >>>>> with "pull_start = yes," in order to take the starting COM >>>>> distance as >>>>> the >>>>> reference. Check the grompp output to verify that you're getting >>>>> what >>>>> you think >>>>> you should be. Otherwise, you'd have to set "pull_start = no" and >>>>> modify your >>>>> .mdp file to reflect the proper value of pull_init1 for every window. >>>>> >>>>> -Justin >>>>> >>>>> >>>>> >>>>> >> >> >
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