Dear Users, I'm trying to do simulations of a particle of varying size in water with my own potential. I've grown a particle by modifying my LJ parameters over time; I know that I can get a particle of 1nm radius and about 2300 TIP4P waters into a box of 4.3x4.3x4.3 with a cutoff distance of 2nm. I want to go to larger particles and “growing” them is too time/computationally intensive.
I tried to use genbox to create the input with the larger volume particles in two different ways unsucessfully. I am using version 3.3.3. (1) I have tried to edit vdwradii.dat to change the radius as follows (I use Ar for the name of my oil particle): .. ??? S 0.16 ??? Ar 1.0 GLY MN1 0 GLY MN2 0 .. However this doesn't seem to have any effect, no matter how large and outlandish I make that number. (2) I've also tired to specify vdw radius using the command line: genbox -cp input.gro -cs tip4p.gro -p topol.top -vdwd 1.0 This seems to work up to about 0.5nm radius and the 4.3 cubic box. If I try to go any larger then I get either a seg fault or the following error: --------------- Program genbox, VERSION 3.3.3 Source code file: ns.c, line: 1938 Fatal error: One of the box vectors has become shorter than twice the cut-off length or box_yy-|box_zy| or box_zz has become smaller than the cut-off. ----------------- I know that if I enlarge the box it will work, but that requires a huge box. Where are the cutoff values that genbox is using coming from? I believe the cutoff is what is giving me such problems as it is doing a cutoff of 3.27 for a radius of 1.0nm. Any hints as to what I'm doing wrong or missing? Thanks, Jill -- Department of Chemistry Purdue University West Lafayette, IN 47907 (765) 494-5591 [EMAIL PROTECTED] _______________________________________________ gmx-users mailing list [email protected] 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
