Can you please let us know exactly how you got the two values that you find to be different (but expected to be the same)? i.e. post your full g_dist command and explain how you observed the value in the output from mdrun. One frame should be enough for now (as long as you are sure -- and can prove to us -- that it is indeed the same frame).
You don't define profile.xvg and I wonder if the discrepancy might be related to your use of pull_start=yes Do you see a consistent bias between mdrun output and g_dist output if you subtract the values for different time frames? If so, is this difference the same as the distance in the initial frame (pull_start=yes)? Chris. -- original message -- I'm a new poster on the maillist, and new to umbrella sampling but not to MD in general. I have recently done some pulling simulation with Gromacs, but have a few questions about the outcome, and in particular the distances that are calculated for the different windows. I realize this is a question that has come up before, and there are some useful posts in the archives, but nothing that exactly answers my questions. To begin, I ran a pulling-simulation pulling a molecule starting in the middle of a membrane (and inside a protein transport channel) straight up in z. To that end, I used the following mdp-settings: pull = umbrella pull_geometry = direction pull_vec1 = 0 0 1 pull_ngroups = 1 pull_start = yes pull_group0 = Protein pull_group1 = pg1 pull_rate1 = 0.001 pull_k1 = 500 So my pull groups are the COM of the protein, and one atom named pg1 on the pull molecule. To my understanding, this should pull the pg1-molecule straight up in z, and that is indeed also what is happening in the simulation. I ran this simulation for 6 ns, and it resulted in about 40 separate conformations to use for umbrella sampling. All of those simulations also seem to work, I can use the resulting pullf,xvg-files as input to g_wham, and get a histogram-plot with reasonable overlaps. However, I'm trying to understand how the various distances relate to each other. For example, in the profile.xvg-file I get a z-distance for the first frame as 1.761971 nm, while checking with g_dist gives me 1.80833 (for z). Continuing a few frames further, there are still differences, and they appear to be random. How are the distances in the profile.xvg-file computed? The average of the dZ column of the pullx-file for the first frame is 1.75787, which is sort of close to 1.761971, but not quite (and also for the next frames there is no closeness). Sorry if this became a long mail, but I need to understand this in order to be able to progress with my research. Thanks -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
