From: Sunhwan Jo (sunhwan_at_uchicago.edu)
Date: Wed Nov 06 2013 - 08:07:25 CST
James,
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?
Best,
Sunhwan
On Nov 6, 2013, at 12:51 AM, James Starlight <jmsstarlight_at_gmail.com> wrote:
> 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 > restraints/$outputname.dihe
> extraBondsFile restraints/$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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