Hi I am trying to do normal MD-simulation on Urea crystal. Basically, I have a PBC box containing 128 urea molecules of cell-length a=b=2.23nm ,c=1.87nm,Tetragonal unit cell (No solvent in the system) to study the polymorphism of urea crystal.
I faced no problem in EM step. I get the energy minimised structure and run successfully run both NVT and NPT simulation at 300K temperature and 1atm pressure. For the (successful) NPT run, I used anisotropic pressure coupling and the coupling constant and compressibility values I have used in the mdp file are as follows: tau_p = 5.0 compressibility = 4.5e-5 4.5e-5 4.5e-5 4.5e-5 4.5e-5 4.5e-5 ref_p = 1.0 1.0 1.0 0.0 0.0 0.0 My average pressure and average temperature is coming -1.85656 bars and 299.6 kelvin ( very close to the required pressure and temperature ). Now I want to run the simulation with the correct experimental values of the compressibility. I treid to look into the literature but could not find a usable value. Someone suggested that compressibility values as derived experimetally are not exactly applicable to simulation systems of such small size, as the values derived are for bulk crystals. So, I should not worry about the compressibility values at all and use the same value as used for water. Is this a valid argument? For what its worth, when I tried a different value of κ larger than water (0.77,0.12,4.5e-2) the simulation crashed. It would be nice if someone can give some insights on how to run these simulations correctly using GROMACS. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
