[gmx-users] Warning message with 3.3.2 but not 3.3.1

[Ranjani Krishnan]

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

ranjanik at mit.edu

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