[gmx-users] Loop displacement calculation?

SeungPyo Hong sp1020 at gmail.com
Tue Apr 22 07:36:21 CEST 2008

Dear gmx-users,
(This is not related to my previous question about the failure of the
simulation. Now I guess that there are some technical problems in our
cluster system.)

Hello gmx-users,  I am not a quite new user, but still don't know many many
Planning an experiment I hope to listen to your advices.

Recently I plan to perform free energy calculation to test the stability of
a loop in a protein.
To do so, I will select two atoms; one in the backbone atom of the loop and
the other in the backbone of the protein nearby the loop region.
Then, those sites are connected by a [ bond ] and the spring constant will
be changed from 0 to 100 as lambda changes from 0 to 1. (The equilibrium
length is fixed to 20 A.)

I am wandering  whether this simulation will be generally accepted or not.

Thank you for your attentions.

'God used beautiful mathematics in creating the world.'
-Paul Dirac
'But he created too many objects.'
-Seungpyo Hong

Seungpyo Hong
Master student at PBIL(Protein BioInformatics Lab.) in KAIST, Daejeon Korea
Tel. (82)-18-372-2468
sphong_ at kaist.ac.kr
sp1020 at gmail.com
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