From: Shadi Rahnama (master.shadi_at_gmail.com)
Date: Sat Jan 25 2020 - 14:56:57 CST
Dear NAMD users;
I am trying to pull a trimmer proteins from a lipid bilayer. I have
selected 700 atoms from each segments and marked them as SMD atoms. I
supposed that NAMD should calculate the center of mass of all selected
atoms from all these segments and put the dummy atom at this place at the
beginning of the simulation. However it seems that other things is going to
be happened!! Here I put the first line of Log file, showing very huge
amount of force at time = 0!!
TCL: Running for 5500000 steps
SMDTITLE: TS CURRENT_POSITION FORCE
SMD 2256000 -1.4053 1.94927 55.2939 0 0 11731.2
It reported 11731.2 pN at the begining, while I expected it should be zero
at this time.
I have select the SMD atoms from "*.restart.coor" file of my production
run, so the initial position of whole system and the positions in reference
SMD file is identical. I could not figure out the problem, is anybody
having any suggesting in this regards?
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