Hi, > Yes. You can use GROMACS to simulate traffic if you want to. :-)
Mark, do you have a force field for that? >> As i had done it with 4 residue with blocking group. But then i got the >> error for rvdw and rlist as they should be nearer to cutoff value. >> So instead of decreasing the value of rvdw. i increased my X, Y, Z >> coordinates. >> Tell me whether i m correct or not. > > We can't possibly tell because we don't know > a) your objective and > b) what sizes you've tried, and > c) what force field you're trying to use, and > d) what errors you've received and > e) what other problems you've encountered. > f) how you've tried to solve the above. Well, probably this is due to the fact that you only use a 1.0 nm distance from the solute to the wall, which makes the box dimension 2.0+peptide dimension, together being less than twice the cutoff radius used (2*1.4=2.8) for at least one direction. Increasing the box dimensions will solve the problem. If you're going to work with more small peptides, it's good to just set the box at 3 nm or so (editconf -f protein.gro -o out.gro -bt dodecahedron -box 3.0). Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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
