Re: [gmx-users] Print Neighbour list

Thank you for your answer. Unfortunately, that is exactly what I am trying to do. However, what I need is more of a custom neighbour search for specific particle-water interactions (i.e. one atom against all the neighbour water molecules), than a completely new class. And I need to do it at

Re: [gmx-users] Print Neighbour list

Hi, gmx select does this kind of operation already, if what you want to do is not part of the simulation... It is implemented by its own simple but fairly efficient search. The neighbor search code is intended for consumption by the short-range kernels, and you do not want to get involved with

Re: [gmx-users] Print Neighbour list

Thanks for your prompt reply. I wanted to print the neighbour list to better understand the way it is processed. I am currently trying to modify the Gromacs code in order to print only the neighbour list of the water molecules around a certain atom. I got inside the code and I found the

Re: [gmx-users] Print Neighbour list

Hi, That's only supported by the group scheme, which is not the default in 2018.3. Probably the output would only be useful from a single-rank run, because the searching might be done and reported in terms of indices of atoms local to the domain being searched, rather than global. Mark On Mon,

[gmx-users] Print Neighbour list

Dear Gromacs community, I am trying to print the neighbour list of my simulations. Following the manual, I added the GMX_DUMP_NL environment variable in my .profile bash file (export GMX_DUMP_LN=1). However, I cannot see any neighbour list printed in my .log file. I am sure that the env

Re: [gmx-users] Print neighbour list

Hi, In the code, it wants you to set GMX_DUMP_NL > 0. And please do everyone a favour and use a version of GROMACS that isn't over five years out of its supported lifetime :-) Mark On Sat, Feb 17, 2018 at 12:07 AM fabio trovato wrote: > Hi, > > I am trying to output

[gmx-users] Print neighbour list

Hi, I am trying to output the neighbor list calculated during a simulation. I consulted the manual which says that DUMPNL is the env variable suited for this purpose. In my bash script I first set up: export DUMPNL=10 and then run the simulation (GROMACS version 4.5.4). I do not see any