[gmx-users] Wierd results from Umbrella sampling

[Du Jiangfeng (BIOCH)]

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