[gmx-users] Position restrain in umbrella sampling

rose rahmani rose.rhmn93 at gmail.com
Wed Jun 6 17:18:41 CEST 2018


I'm doing umbrella sampling for different distances of amino acid from
I know that dear Justin warns people that position restraint was for that
specific situation in the article mentioned in tutorial and ....
I know it doesn't make a sense in my system too in PULLING. But i don't
understand why it's not usable for the rest; i mean in nvt_umbrella for
each window and conformation. I extract different conformations to show the
potential of mean force on that exact distance. So if i don't use position
restraint for AA in for example 0.5nm distance from surface so i can't
claim that this nvt_umbrella run is showing the system manner in a
situation that AA is about 0.5 from surface because without position
restraint(for AA) the AA can be anywhere in box ... . ( i should mention
that surface is frozen in my system)Would you please correct me if i'm

Best regards

More information about the gromacs.org_gmx-users mailing list