<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;">Hi,<br><br>I set my .mdp file to minimize the system for 1000 steps, but it stopped at ~200 saying: "Stepsize too small, or no change in energy.<br>Converged to machine precision, but not to the requested precision Fmax < 10" but the molecule is now outside the box<br><br>I did position restraint for 2ns using LINCS, and things went well<br><br>running md, it ran for only 0.3 ns out of 30, and I got an error message that 1-4 interaction between 2 atoms are at a distance > table-size (1nm) with a suggestion to increase the table-extension in mdp file.<br>I checked http://www.gromacs.org/Documentation/Errors#1-4_interaction_not_within_cut-off suggesting reminimizing. <br><br>My question is: is it OK that the system doesn't minimize till the end of the specified number of steps? is it OK to be outside the box as long as you assign boundary conditions
as in case of NAMD? and what is the best option - you think - I have to solve the md problem<br><br>Any suggestions are highly apprecitaed<br>Rabab<br></td></tr></table><br>