[gmx-users] Bond constraints during the equilibration for membrane-protein system

[li lv]

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.




The similar method was employed in the NPT equilibration and here is one of
the mdp files:

“

title = NPT Equilibration

define      = -DPOSRES

integrator = md

nsteps     = 100000

dt = 0.0005

nstxout = 100

nstvout = 100

nstenergy = 100

nstlog      = 100



continuation    = yes

constraint_algorithm = lincs

constraints = none

lincs_iter = 1

lincs_order = 4



ns_type = grid

nstlist = 5

rlist = 1.2

rcoulomb = 1.2

rvdw = 1.2

coulombtype = PME

pme_order = 4

fourierspacing = 0.16



tcoupl     = Nose-Hoover

tc-grps = Protein DPPC SOL_NA+

tau_t = 0.5      0.5   0.5

ref_t = 323    323  323



pcoupl = Parrinello-Rahman

pcoupltype = semiisotropic

tau_p = 2.0     2.0

ref_p = 1.0     1.0

compressibility = 4.5e-5 4.5e-5



pbc = xyz



DispCorr = EnerPres



gen_vel = no

gen_temp = 323

gen_seed = -1



nstcomm = 1

comm-mode = Linear

comm-grps = Protein_DPPC SOL_NA+



freezegrps = Protein-H

freezedim = Y Y Y

”



Hope those information may help you and others understand my problem.


Li
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