From: James Starlight (jmsstarlight_at_gmail.com)
Date: Wed Nov 06 2013 - 09:02:45 CST
the RMSD have gradually increased during x-y diffusion and then stabilized
when protein have reached position. I suppose that Its more appropriate to
measure msd => Diffusion coefficent (not RMSD) from such trajectory but I
cant find this possibility in namd. By the way what barostat options could
prevent such diffusion ? ( I've tried to increase constant for coupling to
P_bath but there were no any changing).
by the way what exactly role of the restrains in the equilibration steps
(some of them are defined via ColVars as I noticed)?
2013/11/6 Sunhwan Jo <sunhwan_at_uchicago.edu>
> STEP7 inputs provided by CHARMM-GUI comes with no restraints. Under such
> condition, I believe diffusion along membrane is normal. You should be able
> to recenter the protein from the trajectory if needed.
> Your comment about increased RMSD is interesting, though. Are you
> calculating RMSD after reorientation?
> On Nov 6, 2013, at 12:51 AM, James Starlight <jmsstarlight_at_gmail.com>
> > Dear all,
> > As I've mentioned I had problems with the simulation of the
> protein-membrane complex made in Charm-gui. Briefly I had no problems
> during all equilibration phases but on the 7.1 ptoduction run step l've
> observed the diffusion of the protein as the whole (!!!) in the x-y plane
> of the membrane (analysis of the RMSD provides me hight increase in RMSD
> (up to 10A) during first 2ns when such 2D diffusion have been detected).
> I'm not sure if this simulation was OK because I've never seen such motion
> in X-Y plane (previously making long simulation in Gromacs with Langevins
> dynamics and Parinello's barostat). As I've mentioned such motion is
> observed during 7.1 step ( here any restraints are removed from the conf
> file like
> > # planar restraint
> > colvars on
> > exec sed -e "s/Constant \$fc/Constant 0/g"
> membrane_lipid_restraint.namd.col > restraints/$outputname.col
> > colvarsConfig restraints/$outputname.col
> > # dihedral restraint
> > extraBonds yes
> > exec sed -e "s/\$FC/0/g" restraints/dihe.txt >
> > extraBondsFile restraints/$outputname.dihe
> > Does I need more prolonged equilibration in case where I simulate
> protein inserted in the membrane ( in comparison to the pure bilayer) or
> may be some additional restrains should be included in the 7.1 production
> run as well ?
> > James
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