Hello dear gmx-users, I am trying to create a system which has 2,5-dihydobenzoic acid (DHB) as the solvent ( with a positively charged protein and few DHB anions) in a box.
I have created the .itp and .gro file of DHB using PRODRG. I am able to create the system, but when I try to energy minimize the system I get the message: Steepest Descents: Tolerance (Fmax) = 1.00000e+01 Number of steps = 50000 Step= 14, Dmax= 1.2e-06 nm, Epot= 9.04353e+19 Fmax= inf, atom= 2781 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax < 10 Double precision normally gives you higher accuracy. writing lowest energy coordinates. Back Off! I just backed up em.gro to ./#em.gro.1# Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax < 10. Potential Energy = 9.0435262e+19 Maximum force = inf on atom 2781 Norm of force = inf The reason behind this was that DHB molecules were on top of each other, highly dense system ( viewed in VMD) So, to reduce the density of DHB molecules, I tried using-vdwd option of genbox (changed from default value of 0.105 to 0.5) But, I got almost same number of DHB molecules using genbox. What is the best solution to this problem as I understand, reducing the density of DHB molecules around the protein as a solvent or there is some other problem? Thanks in advance, SN
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