[gmx-users] Fwd: reproducibility of PMF plot with two different starting structures?
ammasachu at gmail.com
Fri May 21 08:41:41 CEST 2010
I just want to know about the consistency we could obtain in plotting PMF.
I am using Gromacs 4.0.4 MPI version. Trying to find the PMF of the ligand
transport through the channel. I tried two SMDs (same pull rate, and force
constant) with different starting structures (only ligand poses and
position are slightly different). I performed the sampling of these two
pathways, the plots obtained are of similar overall shapes, but peaks (max
, min) have some variations?
Could you please give your comment on this attempt? Is that expectable?
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