Hello, I am having some trouble using distance restraints. My goal is to apply a harmonic potential to the distance between two atoms in a short peptide (35 residues). Doing simulations in vacuo, both of the following techniques worked to restrain the distance. Also, both techniques worked for simulations in water without periodic boundary conditions. As soon as I include pbc = xyz in my .mdp file and use PME for the electrostatics, my simulation crashes (producing step0.pdb and step-1.pdb). I am assuming this is because GROMACS is using the distance to the image of the other atom, not the actual distance in the box? Is there any way of getting around PBC for distance restraints?
Specifically, I have used the following: 1. I have tried using bonds type 6 in my topology: [ bonds ] ; ai aj funct c0 c1 c2 c3 9 413 6 8.18 421.54 2. When using distance restraints, I added the following lines to my topology file: [ distance_restraints ] ;ai aj type index type low up1 up2 fac 9 413 1 0 1 8.18 8.18 10.0 1.0 In the case of using [ distance_restraints ] in the topology file, I have added the following lines to my .mdp file: disre = simple disre_fc = 421.54 disre_weighting = equal disre_tau = 0 (and various other values of the force constant, disre_fc, but in all cases the run crashes). Thanks for any suggestions! _______________________________________________ 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
