Dear All, While simulating a protein in a box of solvent, I know that the box size should be twice the length of the cut-off. So, if I am using a van der Waals cutoff of 1.4, does it mean that the box dimension should be atleast 2.8 nm from the periphery of the protein?
Secondly, in the experimental conditions, my protein concentration is 1 mM. This accounts to 1 protein molecule occupying 1660 nm^3. For such a volume, I have to generate a box with -d = 3.7 in editconf. I feel that the box is too large and may compromise my computational time. Please comment -Aditi Borkar, TIFR _______________________________________________ gmx-users mailing list [email protected] http://lists.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
