From: Kevin C Chan (cchan2242-c_at_my.cityu.edu.hk)
Date: Wed Apr 19 2017 - 08:20:03 CDT
Dear Users,
I am trying to restart a SMD simulation from some restart file (so
previously also a SMD simulation with same pulling velocity). With all the
same parameters except replacing the starting structure, velocities and box
size (NVT actually), the SMD log tells that the protein is going at the
opposite direction towards the very original starting position. Here's part
of the log (grep SMD output.log):
Info: SMD ACTIVE
Info: SMD VELOCITY 1e-05 ANGSTROM/TIMESTEP
Info: SMD DIRECTION 0.0995037 0 -0.995037
Info: SMD K 7
Info: SMD K2 0
Info: SMD OUTPUT FREQUENCY 1000 TIMESTEPS
Info: SMD FILE smd.pdb
Info: 1766 SMD ATOMS
SMDTITLE: TS CURRENT_POSITION FORCE
SMD 0 46.2727 -22.4778 55.2888 -819.502 0 8195.02
SMD 1000 45.8089 -22.5233 57.9358 -689.32 0 6893.2
SMD 2000 45.6497 -22.6352 61.3402 -524.136 0 5241.36
SMD 3000 45.3855 -22.8015 64.3499 -377.451 0 3774.51
SMD 4000 45.023 -23.0395 66.3123 -280.725 0 2807.25
SMD 5000 44.7117 -23.1445 68.2928 -183.371 0 1833.71
SMD 6000 44.7115 -23.1921 69.4646 -126.463 0 1264.63
SMD 7000 44.5231 -23.1581 70.1801 -90.6157 0 906.157
SMD 8000 44.5002 -23.0958 71.0262 -49.2786 0 492.786
SMD 9000 44.5643 -23.1946 71.3726 -32.425 0 324.25
SMD 10000 44.5897 -23.5262 71.626 -19.8582 0 198.582
So you can see the Z-position goes from 55 back to 71 (the direction should
be [1 0 -10], which points to negative Z) where the protein started from.
Can anyone shares your experience on this?
Note that, I am still using the old "SMDFile" in which atoms to be pulled
where marked by occupancy column. This old "SMDFile" of course contains the
original positions of all atoms. Would this matter?
Thanks in advance,
Kevin
City University of Hong Kong
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