From: Himanshu Khandelia (hkhandel_at_dtc.umn.edu)
Date: Mon Mar 06 2006 - 14:06:35 CST
During equilibration of a transmembrane peptide-bilayer system, I want to
avoid water entering the bilayer, mainly because I need the system to
equilibrate to the right area before running contraint-free dynamics. Is
there a way to setup planar harmonic constraints in NAMD ?
If not, I guess I will have set up constraints on all waters during
If so, will the simulation crash if the area of the bilayer/peptide
assembly shrinks ?
Thanks a ton for the inputs !
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On Sun, 5 Mar 2006, Himanshu Khandelia wrote:
> I was wondering if it was possible to have started a simulation in charmm,
> and continue it in NAMD ? I have already crossed equilibration and am into
> production while using charmm. Given that the force fields are the same,
> will this cause problems ? Importantly, will I be able to use the charmm
> restart file in NAMD ? If not, I will obviously have to restart the
> simulation run from scratch. Thank you very much for your inputs,
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