[gmx-users] Umbrella sampling - position restraints

rookie417 surampudi3 at gmail.com
Thu Aug 8 21:57:50 CEST 2013

Dear GROMACS users,

I followed the Umbrella Sampling tutorial to run a simple simulation of
pulling polymer chain from the surface of micelle. I used position
restraints for the initial equilibration, however I realized a typo in the
define=-DPOSRES mdp files for pulling, US_NPT and US_MD simulations later
during analysis. The simulations ran normally and the PMF plots look
accurate. However, I realized that position restraints were not applied only
after looking at the log files and position restraints energy values were
missing. The umbrella sampling MD simulation was for 2 ns only and I checked
the pullx-umbrella.xvg files and the COM fluctuations are not that bad
considering its only a short time for convergence. 

Can anyone comment on how not using position restraints would effect the
result otherwise?


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