Re: [gmx-users] OPLS3 forcefield

Not sure about OPLS3, but for the publicly available OPLS-AA there are many resources, because OPLS in general is a bit of LEGO. My favorites: 1. http://www.aribeiro.net.br/mktop/ -- sets all atomic charges to zero, unless you supply a list of manually selected charges. You can get charges fro

[gmx-users] The problem of adding 4 peptides in CHARMM-GUI

Dear All,I want to set 4 peptides in DPPE membrane by CHARMM-GUI but just one of them added on DPPE. What must I do? Thanks,Ganj -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://ww

[gmx-users] help with orientation restraints

Hi all;I am an amateur gromacs user, but i have read all the tutorials i could find on how to perform md simulations using gromacs, however i still cant find any tutorial about how to include orientation restraints in my simulations. i want to perform a simulation on a helical protein and includ

Re: [gmx-users] Problem with CUDA

Sorry, forgot to mention that for dynamic linking you (might?) need export CRAYPE_LINK_TYPE=dynamic -- Szilárd On Sat, Apr 7, 2018 at 12:09 AM, Borchert, Christopher B ERDC-RDE-ITL-MS Contractor wrote: > Unfortunately using your shortened cmake args, I still get fpic errors. But > it does compl

Re: [gmx-users] GROMACS 2018 MDRun: Multiple Ranks/GPU Issue

Your GPUs are in process exclusive mode which makes it impossible for multiple ranks to use a GPU; see nvidia-smi --compute-mode option. -- Szilárd On Fri, Apr 6, 2018 at 10:14 PM, Hollingsworth, Bobby wrote: > Hello all, > > I'm tuning MDrun on a node with 24 intel skylake cores (2X12) and 2 V

[gmx-users] OPLS3 forcefield

Hi gromacs users, How to generate OPLS3 force field parameters for an organic molecule? I want to build an automated topology file using OPLS3 force field. How to proceed? Thanks, Neha -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GM