Thanks for your replies. I would like to clarify regarding my first questionn. I don't want a g_dist matrix. I would like to get a covariance matrix where the values correspond to absolute distance and not dived into different dimensions. for example say I have a protein with 100 aa and I run g_covar only on Ca I'll get a 300X300 covariance matrix instead of a 100X100 matrix which is what I want. is there any built in command in Gromacs that will give me this?
Thanks, Gideon
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