[gmx-users] Error in Gromacs

msubrata msubrata at iitk.ac.in
Wed Mar 13 05:58:19 CET 2019


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.

More information about the gromacs.org_gmx-users mailing list