From: Uday Chippada (chippada_at_eden.rutgers.edu)
Date: Wed Feb 11 2004 - 16:00:11 CST
Hi all,
I am presently working on a protein complex which has 3 chains. So I
wish to keep 3 atoms(one each from each chain) as fixed and apply
forces on 3 atoms(each end atom in a chain). When I get the output log
file after doing the constant velocity pulling, I see lines like
SMDTITLE: TS CURRENT_POSITION FORCE
SMD 0 12.5693 21.4467 0.946619 0.000498676 0.000469533 0.0228938
PRESSURE: 0 0 0 0 0 0 0 0 0 0
GPRESSURE: 0 0 0 0 0 0 0 0 0 0
ETITLE: TS BOND ANGLE DIHED
IMPRP ELECT VDW BOUNDARY
MISC KINETIC TOTAL TEMP
TOTAL2 TOTAL3 TEMPAVG
ENERGY: 0 45.3253 200.0123 136.1517
4.6282 429.9201 -34.4355 0.0000
0.0000 203.1495 984.7516 325.5716
986.9983 986.9983 325.5716
OPENING EXTENDED SYSTEM TRAJECTORY FILE
SMD 10 12.5468 21.4616 0.930659 0.0655081 0.0616797 3.00742
SMD 20 12.5203 21.4081 0.950263 -0.230185 -0.216733 -10.5676
SMD 30 12.5153 21.3783 0.949527 -0.320659 -0.301919 -14.7211
SMD 40 12.5201 21.3838 0.971165 -0.657868 -0.619421 -30.2021
SMD 50 12.5606 21.2963 1.0227 -1.29959 -1.22364 -59.6629
Info: Initial time: 1 CPUs 0.00902 s/step 0.0521991 days/ns 0 kB memory
SMD 60 12.5697 21.2662 1.06249 -1.82213 -1.71564 -83.6524
SMD 70 12.565 21.2371 1.09854 -2.30221 -2.16766 -105.692
SMD 80 12.557 21.2927 1.05116 -1.91685 -1.80483 -88.001
SMD 90 12.5592 21.2951 1.04479 -1.95636 -1.84203 -89.8149
SMD 100 12.5878 21.3275 1.07994 -2.44793 -2.30487 -112.382
and many more like this. So my question now is that, how would I know
which SMD atom belongs to which chain.
Thank you
Uday Chippada
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