[gmx-users] number of water molecules affects the PMF

Hi Chris, The two setups were different from each other in terms of only the number of water molecules. Even the starting conformations for the two peptides were the same. I especially took care about that to leave only the number of molecules as a variable. I calculated the error by dividing

Re: [gmx-users] number of water molecules affects the PMF

On Jun 2, 2010, at 9:49 AM, Ozge Engin wrote: Hi Chris, The two setups were different from each other in terms of only the number of water molecules. Even the starting conformations for the two peptides were the same. I especially took care about that to leave only the number of molecules

[gmx-users] number of water molecules affects the PMF

Hi all, I am trying to calculate the potential of mean force between the two hydrophobic dipeptides (phenylalanine) in bulk water via constraint pulling simulations. First, I calculated the mean force at each of the constraint points, and then I integrated the mean force curve to get the PMF. In

Re: [gmx-users] number of water molecules affects the PMF

On Jun 1, 2010, at 9:13 PM, Ozge Engin wrote: Hi all, I am trying to calculate the potential of mean force between the two hydrophobic dipeptides (phenylalanine) in bulk water via constraint pulling simulations. First, I calculated the mean force at each of the constraint points, and

[gmx-users] number of water molecules affects the PMF

It depends on how you generated your error bars and how different your two setups were other than different numbers of water. Xavier's suggestion to split the sampling in half and report each half to the list remains an important piece of data for us to have. Also, please don't reply to