[gmx-users] gmx trjconv

Dear All, I have converted a xtc file into gro file and then want to analyse it with my own fortran code. The same calculation can be done with gromacs commands from xtc file. My question is will I miss some sort of data if I use gro file as there is a precision issue between xtc and gr

Re: [gmx-users] problem regarding gmx trjconv

On 5/2/19 6:59 AM, Saumyak Mukherjee wrote: Dear All, I have an insulin hexamer, which (because of PBC) apparently breaks into pieces after simulation. To make the molecule whole, I use the following command: gmx trjconv -f traj.xtc -s md.tpr -o traj_whole.xtc -pbc cluster or gmx trjconv

Re: [gmx-users] multiple replica trajectory analysis

On 5/2/19 3:19 AM, vijayakumar gosu wrote: Dear Gromacs users, I have simulated a phosphorylated protein with 3 replicas (for 300ns). I concatenated the three replicas (total 900ns) for the analysis (1_2_3_trj_50ps.xtc). When I perform analysis the protein does not include the 3 phospho resi

Re: [gmx-users] gmx trjconv does not produce exact .gro file (slightly different box length)

On 5/2/19 5:13 AM, Faezeh Pousaneh wrote: Hi, I notice that gmx trjconv does not produce the exact .gro file (slightly different box lengths). I mean when i run following command gmx trjconv -f NPT.trr -s NPT.tpr -o f.gro -pbc mol -b 2000 I get slightly different box length than whe

[gmx-users] Electric field applied to a water box

Dear all, I tried to apply a static electric field across a water box. I used anisotropic pressure coupling. Details of the pressure coupling is given below. pcoupl = Parrinello-Rahman pcoupltype = anisotropic tau_p = 5.0 compressibility =

[gmx-users] problem regarding gmx trjconv

Dear All, I have an insulin hexamer, which (because of PBC) apparently breaks into pieces after simulation. To make the molecule whole, I use the following command: gmx trjconv -f traj.xtc -s md.tpr -o traj_whole.xtc -pbc cluster or gmx trjconv -f traj.xtc -s md.tpr -o traj_whole.xtc -pbc mol

Re: [gmx-users] Membrane-protein Simulation

Yes it is normal to correct .xtc file through -pbc flag On Thu, May 2, 2019, 12:57 PM Sankaran SV . <119013...@sastra.ac.in> wrote: > Dear all, > > We are investigating the hydration dynamics of membrane proteins (AQP > embedded in DPPC membrane). The topology and the mdp files for simulations >

Re: [gmx-users] multiple replica trajectory analysis

When you are trying to join two .xtc files phosphorylated residues will be broken. They remain intact when you generate the pdb files or any other analysis.xvg from one and single .xtc file that you have suggested before running md simulation On Thu, May 2, 2019, 12:19 PM vijayakumar gosu wrote:

[gmx-users] gmx trjconv does not produce exact .gro file (slightly different box length)

Hi, I notice that gmx trjconv does not produce the exact .gro file (slightly different box lengths). I mean when i run following command gmx trjconv -f NPT.trr -s NPT.tpr -o f.gro -pbc mol -b 2000 I get slightly different box length than when I run gmx energy ... and select box-X,Y,Z.

[gmx-users] Membrane-protein Simulation

Dear all, We are investigating the hydration dynamics of membrane proteins (AQP embedded in DPPC membrane). The topology and the mdp files for simulations was obtained from the MemprotMD database (mdp file: http://memprotmd.bioch.ox.ac.uk/). We modified the temperature of simulation to 310 K since

Re: [gmx-users] Gromacs 2019.2 on Power9 + Volta GPUs (building and running)

Power9 (for HPC) is 4-way SMT, so make sure to try 1,2, and 4 threads per core (stride 4, 2, and 1 respectively). Especially if you are offloading all force computing to the GPU, what remains on the couch may not be able to benefit from more than 1-2 threads per core. -- Szilárd On Thu, May 2, 2

[gmx-users] multiple replica trajectory analysis

Dear Gromacs users, I have simulated a phosphorylated protein with 3 replicas (for 300ns). I concatenated the three replicas (total 900ns) for the analysis (1_2_3_trj_50ps.xtc). When I perform analysis the protein does not include the 3 phospho residues. However when I analyzed each replica inde