Robert, > 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:
An absolute free energy? This isn't necessarily straightforward -- there are a lot of wrinkles. Some of my recent work has some discussions if this if it's helpful. > 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. OK, that's a good idea for standard state reasons (see the 2003 Boresch paper) among other things. > 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. OK. I have some information posted on what I think the best settings are for these on alchemistry.org, especially at http://www.alchemistry.org/wiki/index.php/Best_Practices. It is still in progress but may be somewhat helpful. I doubt this is the source of your problems though, although I prefer a sc_alpha = 0.5 which may improve the situation somewhat. > 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): Hm, on the position restraints, depending on your version of gromacs you may need to additionally specifiy the B state position restraints, else these may be assumed to be zero. I believe you can do this by adding additional columns in your posre.itp that give the B state parameters. In terms of distortion, it's not clear to me why you think the molecule should *not* be distorted once you turn off the LJ interactions (which includes internal LJ interactions). The bonded parameters (especially torsions) are of course derived after LJ parameters are already fitted, in most cases, so they only can be relied on to give meaningful conformations when the LJ interactions are on. The beauty of the thermodynamic cycle approach, though, is that you can (at least in principle) get correct binding free energies even if your molecule of interest samples wacky, artificial conformations when it's noninteracting. > 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. My experience has been that sc-alpha = 0.7 can lead to a fairly steep dV/dlambda and some large forces near lambda=1, which is why I recommend sc-alpha = 0.5. This parameter is actually fairly sensitive. This *could* lead to crashes, but I don't know about freezing/vibrating. Let me know if this helps. Best wishes, David Mobley UCSF http://www.dillgroup.ucsf.edu/~dmobley > Can anyone comment on what's going on here? > Thanks, > Bob Johnson > _______________________________________________ > 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 [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > _______________________________________________ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
