[gmx-users] Should I fix my drugs during membrane penetration simulation?

yoochan yuchan.m at gmail.com
Sat May 30 07:25:49 CEST 2015

Dear all,

I’m trying to do umbrella sampling simulation which drugs penetrate the POPC membrane.

I have trouble what if I do npt or umbrella simulation, the drugs move around from the initial location.
(I got each 0.1 nm spacing window for npt and umbrella simulation)

So, these results cannot have suitable G_WHAM analysis because of lack of results files at the certain coordinates.

Should I have to fix the drugs to keep and satisfy G_WHAM analysis?

Here I linked my  simulation results and mdp files.

1.) npt_and_umbrella Simulation results.
https://www.dropbox.com/s/w2gq3y686kmw3uc/npt_vs_umbrella_1.png?dl=0 <https://www.dropbox.com/s/w2gq3y686kmw3uc/npt_vs_umbrella_1.png?dl=0>

2) npt.mdp
https://www.dropbox.com/s/y1tg4fhxk6mcpul/npt.mdp?dl=0 <https://www.dropbox.com/s/y1tg4fhxk6mcpul/npt.mdp?dl=0>

3) umbrella.mdp
https://www.dropbox.com/s/0n8bp5rlu6olz3i/umbrella.mdp?dl=0 <https://www.dropbox.com/s/0n8bp5rlu6olz3i/umbrella.mdp?dl=0>

Many Thanks,


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