Hello everyone, I'm computing the relative binding free energies of DNA bases on a nanotube using the protocol listed here: http://www.dillgroup.ucsf.edu/group/wiki/index.php/Free_Energy:_Tutorial I'm using the following steps: 1. Turn off all charges on base 2. Transform LJ parameters 3. Turn on all charges
Because the transformation (from G to A for example) involves changing every single atom charge, I decided to first reduce all charges to zero. The problem I'm experiencing occurs at small lambda values during step 2 (transforming LJ parameters) of the above routine. I obtain large dV/dlambda values of about 2E3 for lambda 0.05 or less. The rest of the curve contains dV/dlambda of about 6E2. I don't think this is due to any equilibration issues. Each lambda point is run for 15 ns and I incur a small error of ~1E-1 for each dV/dl value. The error is a little bit larger (~1) for the lambda=0 point. I believe the topology and simulation protocol is correct. I have already run calculations for the absolute binding free energy of this system and I get good agreement for steps 1 and 3. However, it seems that step 2 is problematic. If I can't get rid of the large dV/dlambda value, how should I handle that? Is this large value an artifact? Or should I assume that the "real" dV/dl curve can be extrapolated to a value that is more reasonable and in better agreement with the rest of the curve? If anyone has some suggestions on how to alleviate this problem, I'd appreciate reading them. Thanks, Bob _______________________________________________ gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
