li lv wrote:
Dear Justin
Thanks for your reply. Generally I conduct the simulation following the
tutorial on your website. The system contains an integrin alpha2b/beta3
transmembrane portion (PDB 2KNC) embedding in a 124-lipids DPPC bilayer
and solvated in water. The initial membrane-protein system is built with
INFLATEGRO. Here is the topology file of the system (not completed):
“
; Include forcefield parameters
#include "ffG53a6_lipid.itp"
; Include chain topologies
#include "topol_A.itp"
; Include Position restraint file
#ifdef POSRES
#include "posre_A.itp"
#endif
#include "topol_B.itp"
; Include Position restraint file
#ifdef POSRES
#include "posre_B.itp"
#endif
; Include DPPC chain topology
#include "dppc.itp"
; Include water topology
#include "spc.itp"
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif
; Include generic topology for ions
#include "ions.itp"
[ system ]
; Name
Protein in water
[ molecules ]
; Compound #mols
Protein_A 1
Protein_B 1
DPPC 124
SOL 17185
NA+ 2
”
For the details of energy minimization, here is one of the mdp files for
energy minimization:
“
define = -DPOSRES
integrator = cg
emtol = 500.0
emstep = 0.01
nstcgsteep = 100
nsteps = 50000
nstlist = 1
ns_type = grid
rlist = 1.2
coulombtype = PME
rcoulomb = 1.2
rvdw = 1.2
pbc = xyz
freezegrps = Protein-H
freezedim = Y Y Y
”
As you may notice, I froze the heavy atoms of the protein during the
first energy minimization and then in the following the EMs the frozen
group was MainChain, C-alpha and none in order. The system finally
reached Fmax < 500.
But do you maintain position restraints? Restraints during minimization serve
little use, and they actually are probably preventing some necessary structural
changes from happening. I'd suspect that's the reason for your instability -
you're not minimizing as well as your system requires.
I would also say that there is no point in using both freezegrps and position
restraints during equilibration, especially NPT, where freezegrps actually
interfere with proper coordinate scaling. I would suggest you simply use
position restraints.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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