Re: [gmx-users] gmx distance

Documentation on how to use the selections can be found at http://manual.gromacs.org/current/onlinehelp/selections.html What you will need here is something to uniquely identify each of the residues (and atoms?) in the two proteins. Run the script just on a coordinate file when working out what t

Re: [gmx-users] extra-bond

Hi, Look for [ intermolecular_interactions ] in the manual! Mark On Sun., 10 Mar. 2019, 11:23 Stefano Guglielmo, wrote: > Thanks for quick reply Justin; as the atom pairs come from two molecules, > is pdb2gmx the only way to merge different molecules in a single [ > moleculetype ]? I got some

Re: [gmx-users] info about gpus

There is significant information on the web regarding this subject, but in general speed scales nicely with the umber of cores. Massive memory is not required. > On 31,Jan 2019, at 11:14 AM, Stefano Guglielmo > wrote: > > Dear all, > I am tryin to set a new workstation and I would like to kn

[gmx-users] hydrophobic interactions and electrostatic interactions between the protein chains

Hi dear GROMACS usersI want to calculate  hydrophobic interactions and electrostatic interactions between the protein chains using gromacs trajectory  . Please guide me.Thanks a lot -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-U

Re: [gmx-users] extra-bond

Thanks for quick reply Justin; as the atom pairs come from two molecules, is pdb2gmx the only way to merge different molecules in a single [ moleculetype ]? I got some troubles with it supposingly because the system was generated with Ambertools and then converted, thus pdb2gmx does not recognize p

Re: [gmx-users] info about gpus

Thanks to all of you for sharing opinions and hints, Stefano Il giorno lun 4 feb 2019 alle ore 14:35 Szilárd Páll ha scritto: > On Fri, Feb 1, 2019 at 4:58 PM paul buscemi wrote: > > > > I’ve run these conditions recently. The scale from as single 1080ti to > 2080ti is proportional to the core