Dear Sir/Madam,
I have performed umbrella pulling and umbrella sampling my protein from a
DOPC/DOPS membrane. Unfortunately, the results are really bad (Energy curve
suddenly turns to zero at the last 1 nm) and the histograph does not show any
overlap. Actually, I did it strictly based on Justin's tutorial, with the
sample spacing of 0.2 nm.
Here are some lines from the end of the energy file (The energy should not
decrease since it was in summation):
Distance(nm) Energy (Kcal/mol)
5.288348 5.705318e+01
5.316250 4.881724e+01
5.344152 4.022505e+01
5.372054 3.101854e+01
5.399956 2.208200e+01
5.427858 1.343340e+01
5.455761 4.267619e+00
5.483663 -5.084078e+00 ? minus
5.511565 -1.486168e+01 ? minus
5.539467 -2.393515e+01 ? minus
5.567369 -3.343453e+01 ? minus
Followings are some lines from the end of histograph file:
Distance(nm)
5.455761 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
8
5.483663 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
8
5.511565 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
12
5.539467 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
4
5.567369 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
2
I am really depressed because it took me quiet a long time to sampling but it
seems in vain... I really no idea to find out what went wrong.
I am looking forward to your help. Thanks a lot.
Jiangfeng.
Jiangfeng Du, PhD Student
Cardiovascular Research Institute Maastricht
Department of Biochemistry
P.O. Box 616
Mobile: +31-681741859
FAX: +31-43-3884159
6200 MD Maastricht
The Netherlands--
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