[gmx-users] Fwd: reproducibility of PMF plot with two different starting structures?

Aswathy 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?

Thank you,


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