PBC problem in Steered MD simulation

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.

Hold one end fixed
100.0
ATOM 21
END
END

ncsu_smd
    output_file = 'md2.smd'
    output_freq = 1000
    variable
       type = DISTANCE
       i = (21, 1458)
       path = (X, 3.0) path_mode = LINES
       harm = (100.0)
    end variable
end ncsu_smd

 

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.

 

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