Re: [gmx-users] FEP trajectory errors

Yep, all atoms begin to freezeeven the ones not being perturbed (i.e. the water molecules). It's pretty strange. It only happens for lambda=1.0. Below is my .mdp file. ; Run Control integrator = md ; calculation type dt = 0.0015

Re: [gmx-users] FEP trajectory errors

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. : ++49 551 201 231

Re: [gmx-users] FEP trajectory errors

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

Re: [gmx-users] FEP trajectory errors

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

Re: [gmx-users] FEP trajectory errors

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 simulatio

Re: [gmx-users] FEP trajectory errors

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. So

Re: [gmx-users] FEP trajectory errors

Robert I think, I cant help you too much, cause your problem involves too many sources of errors. Your topology (if continued that way) seems to be ok. Your TI-params seem to be ok, too. First, make clear: Do you use Position RESTRAINTS or (distance) CONSTRAINTS. There is a fundamental differ

[gmx-users] FEP trajectory errors

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