Hi dear gromacs users, I am planning to study the interaction between a SWCNT and the outside of an ion channel, in order to do this i am preparing a Umbrella Sampling Simulation, were i put the CNT, (3nm or 2nm) from the ion channel's pore, and the CNT axis is parallel to the pore axis, in order to compute the PMF between the CNT and the external residues of the ion channel ,
in order to do this i was thinking first just run unconstrained MD of the CNT and understand the potential energy surface, and then run the US using constraints XY (Z axis) due to CNT might move or should i not use constraints at running US ? , I was wondering if you could give me some advice about this, it is my point of view well think? or should i think in a different methodology ? Thank you in advance Andrés -- View this message in context: http://gromacs.5086.x6.nabble.com/SWCNT-interaction-with-the-outside-of-an-ion-channel-tp5016110.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
