Hello everyone, I'm computing the free energy of binding of a DNA base on a carbon nanotube. I think it's a pretty simple calculation and I'm proceeding in a very standard way. This is what I'm doing:
I have the optimal orientation of the base on the nanotube. I'm constraining the positions of the base atoms with a soft harmonic potential. I then am running two different FEP calculations: one where I turn off the charges on the base atoms and a second where I then turn off all the lennard-jones parameters for the base atoms. For each of these I use the following: delta_lambda = 0 sc_alpha = 0.7 sc_power = 1 sc_sigma = 0.3 I run a series of trajectories at constant lambda values from 0 to 1. However, I notice some problems with the trajectories when I turn off the LJ parameters. As lambda is varied from 0 to 1, it seems that the position restraints no longer are being applied. Additionally, the DNA base geometry starts to become severely distorted at lambda values greater than about 0.6. This happens despite the fact that I am not perturbing the internal bonded interactions of the base. Here is a sample of my topology (included just the first line of each section): [ moleculetype ] ; Name nrexcl dg-disappear 3 [ atoms ] 1 P 1 DG P 1 1.1659 30.9700 DUM 0.0000 30.9700 ... [ bonds ] 1 2 1 0.1480 439320.0000 0.1480 439320.0000 ... [ angles ] 1 4 5 1 120.5001 836.8000 120.5001 836.8000 ... [ dihedrals ] 1 4 5 8 1 0.0000 1.6039 3 0.0000 1.6039 3 ... [ position_restraints ] 1 1 100 100 100 100 100 100 ... So you can see that I am not perturbing the bonded interactions as I have just copied the same values from topology A. Also, I am experiencing additional problems when lambda=1. After about 2ns, all the motion in the system begins to freeze and all the atoms simply vibrate about a fixed position. Soon after that the simulation crashes. Can anyone comment on what's going on here? Thanks, Bob Johnson _______________________________________________ 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
