Re: [gmx-users] problems with the output of pullx

Hi all, I want to update my own post for any user that could have similar issues in the future. The issue that I described before (large spikes were observed in the values reported in pullx file but when i calculated the same restrained distance using “gmx distance” no such spikes were

Re: [gmx-users] problems with the output of pullx

Hi Mark, Thanks for your comment. No, that is not the problem. At that location the center of mass of the peptide is deep inside the membrane, separation between the two pulling groups is 0.4 nm and the dimension of the cell along z is more than 10 nm. I am only pulling along the z

Re: [gmx-users] problems with the output of pullx

Hi, My (thoroughly uneducated) guess is that the spikes are related to the pull distance approaching half of the dimensions of the cell. Not all flavours of pulling can handle this. Might that be the issue? Mark On Sat, Feb 24, 2018, 17:55 alfredo wrote: > Hi, >

Re: [gmx-users] problems with the output of pullx

Hi, Updating my post. The problem has been observed in two different machine systems (the latest I have found the problem was the skylake nodes in tacc). I assumed it has to be some communication bug of coordinates and forces in the pull part of the code. Probably observed in my case because