VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Tue Dec 08 2009 - 13:23:59 CST

Hi:
Do restraints on CG models apply like for all-atoms? For example, in
order to restrain the polar head of POPC lipid

ATOM 2463 CHO POPCO 1 37.490 25.415 4.653 1.00 0.00 O1 C
ATOM 2464 PHO POPCO 1 39.740 24.614 0.940 1.00 0.00 O1 P
ATOM 2465 ES1 POPCO 1 37.568 20.460 -0.263 1.00 0.00 O1
ATOM 2466 ES2 POPCO 1 37.020 21.866 -4.322 1.00 0.00 O1
ATOM 2467 ME1 POPCO 1 36.057 16.858 1.933 1.00 0.00 O1
ATOM 2468 ME2 POPCO 1 35.653 13.060 0.274 1.00 0.00 O1
ATOM 2469 ME3 POPCO 1 37.948 9.854 -0.816 1.00 0.00 O1
ATOM 2470 MT1 POPCO 1 38.047 4.914 0.293 1.00 0.00 O1
ATOM 2471 ME4 POPCO 1 35.557 18.929 -6.037 1.00 0.00 O1
ATOM 2472 ME5 POPCO 1 36.308 15.668 -9.314 1.00 0.00 O1
ATOM 2473 ME6 POPCO 1 37.484 11.986 -12.138 1.00 0.00 O1
ATOM 2474 MT2 POPCO 1 37.279 8.543 -12.520 1.00 0.00 O1
END

are restraints to be applied to beads CHO and PHO? If so, by making
the .fix file in VMD as if it were an all-atoms model are the
restraint forces applied correctly?

And if I want to restraint the whole protein and the whole bilayer (to
work at constant pressure on the solvent water around), is any way to
simply specify the range of residue numbers?

That is, I assume to have to prepare the system for production as
carefully as if it were all-atoms.

thanks
francesco pietra