[gmx-users] compressed pbc box at the end of simulation - membrane protein with ligand

Dear all, I am carrying out a simulation of membrane protein with a ligand. I am using DPPC [slipids (http://www.fos.su.se/~sasha/SLipids/Downloads.html)]. I had modified amber 03 ff by including the non-bonded and bonded parameters from slipids website as suggested in the tutorial by Justin (

[gmx-users] Water Density

Hello everyone I did a protein water simulation. I want to calculate water density in both interface and bulk. How can I find this resulte? Thanks -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't

Re: [gmx-users] There is no domain decomposition error

Hi, Thanks Mr. Bauer for your help. Actually, I was running grompp in desktop and the mdrun in cray. Now I am running both in cray and it runs fine. Thanks again. Dhrubajyoti Maji On Mon, 10 Jun 2019 at 20:38, Paul bauer wrote: > Hello, > > did you change the command to submit the

Re: [gmx-users] There is no domain decomposition error

Hello, did you change the command to submit the calculation or did you use a different machine to run the calculations? This error usually means that the domain decomposition can't run on the requested number of (thread)-MPI ranks. Try using a different number of ranks or different

Re: [gmx-users] force field for organometalic compound

Hi, You can use acpype to build the amber forcefield parameters. Each force field have corresponding servers which can make .tpr file for you. You can easily run simulation with that file. On Mon 10 Jun, 2019, 6:43 PM antonia vyrkou, wrote: > Dear all, > > I want to simulate an

[gmx-users] force field for organometalic compound

Dear all, I want to simulate an organometallic compound and how it affects an enzyme's function using Gromacs but I am having trouble finding suitable force field parameters. If would really appreciate any suggestions for a Gromacs compatible , Amber compatible force field Thank you Antonia --

Re: [gmx-users] Density of ligand molecules around a particular residue

gmx rdf should give you this. It will give you the radial distribution function of the ligand molecules about the specific residue. -Micholas === Micholas Dean Smith, PhD. MRSC Post-doctoral Research Associate University of Tennessee/Oak Ridge National Laboratory Center for