Do really all atoms "freeze". So also the atoms, which are not perturbed? Can you post your mdp-file?
Regards
Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Germany
Tel. : ++49 551 201 2310
Fax : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
mgoette2[at]gwdg.de
WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/
Robert Johnson wrote:
The distortion was occuring because my position restraint potential was too weak. Increasing the force constant keeps the base in the right conformation. I believe my topology is correct, but it seems that turning off the VdW parameters causes the base to distort. I will look into this more. Also, even with sc_alpha=0.5, I'm still experiencing this weird "freezing" when lambda=1.0. The trajectory proceeds normally for about 2.1 ns, then all of a sudden all motion freezes and the atoms simply vibrate about their "equilibrium positions". Any other ideas what might cause this? Thanks, Bob On Jan 21, 2008 3:39 AM, Maik Goette <[EMAIL PROTECTED]> wrote:Robert A value for alpha of 0.5 should work, although I tested some different alphas with different test systems and I have to say, that a proper value can be between 0.2 and 0.7 depending on the system itself. The distortion, you describe is really strange. I calculated DNA and single bases a lot and never saw something like that. Even a fully "dummy-base" is stable, if your topology is correct. The bonded terms are sufficient to keep it in the right conformation. Are you sure, your position restrains in the topology are used with the correct structure file? Maybe, I should also mention, that, especially with such large perturbations as a full DNA-base, you should split your topology into 2, where you switch off the QQ hardcore and the VdW softcore in two steps. Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ Robert Johnson wrote:Thank you David and Maik for your detailed replies. Yes, I am trying to obtain an absolute free energy of binding. My thermodynamic cycle is: NT+DNA(adsorbed) -> NT+ DNA(desorbed) (obviously this is not the one that I'm obtaining with the alchemic method) Thus, the one I'm using in the simulation is: Water + NT + DNA(adsorbed) -> Water + NT + nothing (DNA dissapears) Water + DNA -> Water + nothing Any suggestions about this? I will check out your recent publications. I believe my topology is properly formatted. I wasn't expecting the large distortions because I was using position restraints. Thus, I was expecting the base to remain in about the same geometry. Perhaps I will increase the force constant for the restraining potential. I am going to repeat some of these computations using sc_alpha=0.5. Thanks for your help. Bob On Jan 17, 2008 2:24 PM, David Mobley <[EMAIL PROTECTED]> wrote: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/~dmobleyCan 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? 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