<div>Dear List </div><div>I'm newbie to MD .</div><div>I'd like to simulate a protein protein binding dinamic between 2 proteins of 500 aa each one. I have some very basic questions:</div><div>1) In order to setup my dinamic i'm following the basic tutorial on spider toxin peptide (<a href="http://www.gromacs.org/Documentation/Tutorials#Protein-Ligand_Systems">http://www.gromacs.org/Documentation/Tutorials#Protein-Ligand_Systems</a>) starting from a pdb with the 2 structures near each other and oriented according to some docking calculations. Is this procedure a reasonable starting point? </div>
<div><br></div><div>2) I tryed to run the MD with the same parameters of tutorial in my md.mdp file (listed at the end of the mail). Should i set the contraints parameter to "none"? In order to allow more flexibility of the side chains?</div>
<div>Finally if the previous points are reasonable ...</div><div>3) In your opinion which could be a reasonable time to explore the possibility that the 2 proteins bind each other? I'm making some attempts using 500 ps for now </div>
<div><br></div><div>Sorry for my silly questions and thank you very much for any kind of help </div><div>Best </div><div>Guido</div><div><div><div>define = -DPOSRES</div><div>constraints = all-bonds</div>
<div>integrator = md</div><div>dt = 0.002 ; ps !</div><div>nsteps = 50000 ; total 100.0 ps.</div><div>nstcomm = 10</div><div>nstxout = 500 ; collect data every 1.0 ps</div>
<div>nstxtcout = 500</div><div>nstvout = 5000</div><div>nstfout = 0</div><div>nstlog = 10</div><div>nstenergy = 50</div><div>nstlist = 10</div><div>
ns_type = grid</div><div>rlist = 1.0</div><div>coulombtype = PME</div><div>rcoulomb = 1.0</div><div>vdwtype = cut-off</div><div>rvdw = 1.4</div><div>
pme_order = 4 </div>
<div>ewald_rtol = 1e-5</div><div>optimize_fft = yes</div><div>DispCorr = no</div><div>; Berendsen temperature coupling is on</div><div>Tcoupl = v-rescale</div><div>tau_t = 0.1 0.1</div><div>
tc-grps = protein non-protein</div><div>ref_t = 300 300 </div><div>; Pressure coupling is off</div><div>Pcoupl = no</div><div>Pcoupltype = isotropic</div><div>tau_p = 1.0</div>
<div>compressibility = 4.5e-5</div></div><div><br></div><div><br></div>-- <br>Guido Leoni<br>National Research Institute on Food and Nutrition<br>(I.N.R.A.N.)<br>via Ardeatina 546<br>00178 Rome<br>Italy<br><br>tel + 39 06 51 49 41 (operator)<br>
+ 39 06 51 49 4498 (direct)<br>
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