Hello dear gmx-users,<br><br>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.<br><br>I have created the .itp and .gro file of DHB using PRODRG.<br>
<br>I am able to create the system, but when I try to energy minimize the system I get the message:<br><br>Steepest Descents:<br> Tolerance (Fmax) = 1.00000e+01<br> Number of steps = 50000<br>Step= 14, Dmax= 1.2e-06 nm, Epot= 9.04353e+19 Fmax= inf, atom= 2781<br>
Stepsize too small, or no change in energy.<br>Converged to machine precision,<br>but not to the requested precision Fmax < 10<br><br>Double precision normally gives you higher accuracy.<br><br>writing lowest energy coordinates.<br>
<br>Back Off! I just backed up em.gro to ./#em.gro.1#<br><br>Steepest Descents converged to machine precision in 15 steps,<br>but did not reach the requested Fmax < 10.<br>Potential Energy = 9.0435262e+19<br>Maximum force = inf on atom 2781<br>
Norm of force = inf<br><br><br>The reason behind this was that DHB molecules were on top of each other, highly dense system ( viewed in VMD)<br>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)<br>
But, I got almost same number of DHB molecules using genbox.<br><br><br>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?<br>
<br>Thanks in advance,<br>SN<br><br>