Dear gromacs users, I want to perform a pulling simulation of the unfolding of a protein but I am not sure which pull_geometry is the correct one for this problem. First I try using position with pull-dim= Y Y Y, since It will allow the force to have components in the three dimensions, even is the pull_vector is oriented only in one. The problem of this setup is that I need a really large box, at leat all the dimensions should be twice the lenght of my protein, since the pulling code checks that the distance between the pulll and reference group is smaller than 0.49 the large of all the dimension. If I choose pull_geometry= direction I have the same problem.
A possible solution will be to use pull-geometry= position and pull-dim= N N Y, but this will imply that I dont allow the force to have components in the other two dimension, which is unrealistic. Is there a setup which I can used that allows the force to have component in the three dimension and at the same time to use a box that it is only large in the pulling direction? Thank you Lalita -- Lalita S. Uribe. European Master in Theoretical Chemistry and Computational Modeling. PhD student. Johannes Gutenberg-Universität Mainz -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
