Dear gromacs users, <br>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<br> 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 <br>
tried using the following values:<br><br> vdw_type = switch | vdw_type = switch | vdw_type = switch <br>
coulomb_type = PME | coulomb_type = PME | coulomb_type = PME <br> rlist = 1.2 | rlist = 1.3 | rlist = 1.4 <br> rcoulomb = 1.2 | rcoulomb = 1.3 | rcoulomb = 1.4 <br>
rvdw = 1.0 | rvdw = 1.0 | rvdw = 1.0 <br> rvdw_switch = 0.9 | rvdw_switch = 0.9 | rvdw_switch = 0.9 <br><br>
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?<br> I have gone through OPLS papers also but was unable to get a precise answer for my question.<br>
<br>2. What is the type of thermocouple suggested during energy minimization? Berendson or Nose-hoover?<br><br>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?<br>
I am attaching two rmsd plots of backbone after running for 12ns,
Does any of them indicates equilibration? 1st with 1.2nm (rlist =
rcoulomb=1.2nm);<br> 2nd with 1.4nm, 1.2nm except 1.4nm gave the message regarding the sum of charge group radii
being larger<br>
than the rlist - rvdw.<br><br>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?<br> Will it
equlibrate at all? will not the domain movement or movement of a large
loop in the structure prevent it from equilibration?<br>
<br>Kindly Give some suggestions and comments<br><br>Thanking you<br>With Regards<br><font color="#888888"><font color="#888888">M. Kavyashree</font></font>