[gmx-users] Q's regarding cutoff, charge groups, thermocouple and equlibration

[Kavyashree M]

Dear gromacs users,
1.  When one is using OPLSAA force field for simulation a protein of say
100aa to 250aa long protein, TIP4P water model in gromacs 4.5.3
    what are the values of cut offs to be used ie., rcoloumb, rvdw,
rvdw-switch and rlist? I have gone through the manual and papers and
    tried using the following values:

   vdw_type = switch       | vdw_type = switch       | vdw_type = switch

   coulomb_type = PME  | coulomb_type = PME  | coulomb_type = PME
   rlist = 1.2                     | rlist = 1.3                     | rlist
= 1.4
   rcoulomb = 1.2            | rcoulomb = 1.3            | rcoulomb = 1.4

   rvdw = 1.0                   | rvdw = 1.0                   | rvdw =
1.0
   rvdw_switch = 0.9        | rvdw_switch = 0.9        | rvdw_switch =
0.9

   but only last set of values did not give rise to any messages during
grompp regarding charge group radii being larger etc..  Are these parameters
acceptable?
   I have gone through OPLS papers also but was unable to get a precise
answer for my question.

2.  What is the type of thermocouple suggested during energy minimization?
Berendson or Nose-hoover?

3. What is the way to confirm that a system has equilibrated after starting
the production MD? Is it RMSD from the initial structure, or average
structure?
   I am attaching 2 rmsd plots of backbone after running for 12ns, Does any
of them indicates equilibration? 1st with 1.2nm (rlist = rcoulomb);
   2nd with 1.4nm, 1.2nm except 1.4nm gave the message regarding the sum of
charge group radii being larger
   than the rlist - rvdw.

4. If MD is run on a protein which had intrinsic domain motion, how will
that equilibrate during MD? i.e., how will the rmsd plot appear when it is
equilibrated?
    Will it equlibrate at all? will not the domain movement or movement of a
large loop in the structure prevent it from equilibration?

Kindly Give some suggestions and comments

Thanking you
With Regards
M. Kavyashree
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