From: Haleh a (halehabdi_at_sabanciuniv.edu)
Date: Tue Dec 15 2015 - 09:59:10 CST
Dear NAMD users,
I have been trying to calculate free energy changes upon a mutation in a
protein via FEP method. The transformations were subdivided into 32
windows. Each stratum consisted of 100,000 data-collection steps preceded
by 25,000 equilibration steps.
For a few of my mutations the free energy change upon forward and backward
transformations were not the same. An example of a Parsefep file for dG
column is given below:
fw bw
0.0000 19.2024
7.8597 27.3887
15.8585 35.4349
23.8350 42.7734
30.9869 49.8046
38.1433 56.4785
45.1326 63.2339
51.5564 69.8128
57.9795 75.7305
64.2681 81.6443
70.2732 86.9015
76.0547 91.6371
81.0941 95.7292
85.2021 99.6043
88.3743 103.2919
91.4066 106.3001
93.3668 108.3961
91.4244 106.6218
89.3347 104.5966
87.0627 101.5024
84.6330 97.8175
81.7766 93.0725
78.8473 88.2228
75.5645 83.1926
70.4596 77.7998
65.0760 71.9186
59.6825 65.5346
54.1291 59.0037
48.5446 52.6676
42.7863 45.8779
36.9261 38.9123
31.0231 31.7249
25.1445 25.1445
I tried running the simulation with longer data collection and
equilibration time but it did not help. Does anyone have any idea why such
a problem exist and how to solve it?
Many thanks,
Haleh Abdizadeh
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