Hi,
I am running AFM pulling simulations on an integrin-RGD system. I have tried running the exact same simulation in version 3.3.1 and version 3.3.2, and I am getting a large VCM message in 3.3.2, but not 3.3.1. Here are the cases that I have tried: 1) Version 3.2.1: The integrin receptor has two subunits, alpha and beta. If I do com motion removal on these two separately (i.e. comm._grps = alpha beta), with tc_grps = Protein Other, the simulation finishes normally. 2) Version:3.2.2: Same conditions as above, but I get the following message in the log file. This happens even if I use the exact same input files as with version 3.2.1. It starts at the beginning of the simulation and continues to print this message at every output timestep. Large VCM(group rest): 0.00001, -0.00002, -0.00000, T-cm: inf Large VCM(group rest): 0.00001, -0.00003, -0.00000, T-cm: inf Large VCM(group rest): -0.00000, -0.00003, -0.00000, T-cm: inf Large VCM(group rest): -0.00000, -0.00003, 0.00000, T-cm: inf Large VCM(group rest): -0.00001, -0.00004, 0.00000, T-cm: inf Large VCM(group rest): -0.00001, -0.00004, 0.00001, T-cm: inf Large VCM(group rest): -0.00001, -0.00004, 0.00001, T-cm: inf Large VCM(group rest): -0.00001, -0.00004, 0.00001, T-cm: inf Large VCM(group rest): -0.00001, -0.00003, 0.00002, T-cm: inf Large VCM(group rest): -0.00001, -0.00003, 0.00002, T-cm: inf Large VCM(group rest): -0.00001, -0.00003, 0.00002, T-cm: inf Large VCM(group rest): 0.00000, -0.00003, 0.00002, T-cm: inf Large VCM(group rest): 0.00001, -0.00003, 0.00002, T-cm: inf Large VCM(group rest): 0.00002, -0.00003, 0.00002, T-cm: inf Large VCM(group rest): 0.00002, -0.00002, 0.00002, T-cm: inf Large VCM(group rest): 0.00003, -0.00002, 0.00002, T-cm: inf 3) Version 3.2.2: If I try comm._grps = alpha beta and tc_grps = alpha beta Other, this message does not appear. Question 1: What has changed between version 3.2.1 and 3.2.2 that is causing this message to appear? I can't find information about this on the website. Question 2: Is it an adequate solution to make comm._grps the same as tc-grps? Can somebody explain why I no longer have the VCM problem in this case? Thank you very much, Ranjani Ranjani Krishnan Graduate student, Department of Biological Engineering Massachusetts Institute of Technology [EMAIL PROTECTED]
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