Hi all, While running an energy minimization with mdrun 3.3.1, I observed that different peptide units in the simulation box were translated in y direction out of the box, each by N*Ly, N=1,5 (N is peptide unit and Ly is the box y-dimension). The final structure (confout.gro) is a kind of staircase instead of beta sheet which I'm trying to simulate.
Only one peptide and all solvent (water and Cl-) remain in the original box. This happens even after setting nsteps=1. My system is probably quite far from equilibrium but this kind of behaviour seems anyway unexpected. I used genconf to generate the initial structure (which looks fine) and it is these generated units which become translated with mdrun. Any suggestions how to solve this problem are welcome. best regards, Olli _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
