I am using distance of two atoms as CV and Steered MD simulation to force a linear molecular to a ring to calculate the tension on the ring. No matter whether this method was correct or not, I had some problems.
Some command of SMD is below.
Atom 21 was constrained. Atom 1458 could be moved. The finial distance was set to 3 Angstrom.
I measured the initial distance in VMD which was around 122Angstrom. But the output printed out 87Angstrom as initial distance.
I debugged for quite a while. And then I realized this should be caused by PBC, when I was having my lunch (very delicious Chinese Braised Pork Belly ; )
I changed the NPT system to NVT, since my initial coordinate was got from a well equilibrated system.
In detail, change ntb = 2, pres0 = 1.0, ntp = 1, to ntb = 0, igb =0,.
Then the output was normal.