[gmx-users] Umbrella sampling to calculate binding energy under martini force field

[Du Jiangfeng (BIOCH)]

Dear GMX-users,

How about the accuracy of the binding energy calculation by umbrella sampling for a coarse gained system in which a protein domain binding to membrane?

Coarse gained force fields are less accurate if compared with atomistic ones and too many values from it are given by estimation. Also, I was informed from a conference that it is still not reliable of the free energy calculation even in an atomistic system.

So the coarse gained system and free energy calculation are both suspected. Then, what happens if calculating the binding energy in a coarse gained system? Does the result be advisable for a wet experimental work?

Thank you,


    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