Hello gmx users, <div><br><div> I am trying to simulate one protein in solvent with PBC xyz in standard condition (1 atm, 303K). However since I am using Martini force-field, some parameters in P-coupling and T-coupling confuse me a lot. Here are two questions listed below:</div>
<div> 1. What is the compressibility mean? In my simulation can I just use:</div><div> Pcoupl = Berendsen</div><div> Pcoupletype = isotropic</div><div> tau_p = 2.0</div><div> compressibility = 4.5e-5</div>
<div> ref_p = 1.0</div><div> However, in the Gromacs 4.0 manual, it shows "For water at 1 atm and 300 K the compressibility is 4.5e-5 [bar-1]", does it mean I don't have to consider about coarse-grained water molecule difference when setting the compressibility?</div>
<div><br></div><div> 2. For T-coupling, I use "Berendsen" method. After generating the job, there is one note:</div><div> "The Berendsen thermostat does not generate the correct kinetic energy distribution. You might want to consider using the V-rescale thermostat."</div>
<div> What does this note mean? For my system (protein + solvent), will the choice of different T-coupling method be very different for dynamic results?</div><div><br></div><div> Thanks in advance.</div><div> </div>
<div><div> <br clear="all"><br>-- <br>Sincerely<br>=================================<br>Pan Wu<br>Graduate Student in Department of Chemistry<br>Duke University<br>124 Science Drive<br>5301 French Family Science Center<br>
Durham, NC 27708<br>Phone: (919) 660-1583<br>=================================<br><br>
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