[gmx-users] PBC correction to visualize a protein-membrane structure

Dear GROMACS users, I’m preparing a protein-membrane structure to use as input for MD. I’ve just carried out a short minimisation of the lipids applying restraints to the protein, after which I’ve obtained the attached structure. I’ve tried all types of trjconv combinations with -pbc -ur or

[gmx-users] PBC correction to visualize a protein-membrane structure

Dear GROMACS users, I’m preparing a protein-membrane structure to use as input for MD. I’ve just carried out a short minimisation of the lipids applying restraints to the protein, after which I’ve obtained the attached structure. I’ve tried all types of trjconv combinations with -pbc -ur or

Re: [gmx-users] PBC correction to visualize a protein-membrane structure

On 5/16/14, 4:04 AM, Juan Munoz-Garcia wrote: Dear GROMACS users, I’m preparing a protein-membrane structure to use as input for MD. I’ve just carried out a short minimisation of the lipids applying restraints to the protein, after which I’ve obtained the attached structure. I’ve tried all

Re: [gmx-users] PBC correction to visualize a protein-membrane structure

Thank you Justin, please find a dropbox link to the image below. I’ve used trjconv_mpi -f NPT.trr -o NPT_2.trr -s NPT.tpr -pbc whole trjconv_mpi -f NPT_2.trr -o NPT_PBC.trr -s NPT.tpr -pbc mol -ur compact -center and different combinations of those

Re: [gmx-users] PBC correction to visualize a protein-membrane structure

On 5/16/14, 9:08 AM, Juan Munoz-Garcia wrote: Thank you Justin, please find a dropbox link to the image below. I’ve used trjconv_mpi -f NPT.trr -o NPT_2.trr -s NPT.tpr -pbc whole trjconv_mpi -f NPT_2.trr -o NPT_PBC.trr -s NPT.tpr -pbc mol -ur compact -center and different combinations of

[gmx-users] berendsen vs parrinello-rahman

Hello, I am running the simulation for ionic liquids. I initially did simulation with Gromacs VERSION 4.0.7 with parrinello-rahman pressure coupling. Here I pasted temperature and pressure coupling part of mdp file. ; Temperature coupling is on Tcoupl = v-rescale tau_t = 0.1 tc-grps =system

Re: [gmx-users] Degree of hydrogen bonding

Hi Abraham, When I do the indexing, the hbndx gives all h-bonds in ascending order for all frames and i see the a lot of repeated bonding with the same acceptor atom. Is it possible to get the index for a particular frame? I see the option -dt but i didn't quite get that one. Also, the hbnum.xvg

Re: [gmx-users] berendsen vs parrinello-rahman

On 5/16/14, 11:37 AM, Nilesh Dhumal wrote: Hello, I am running the simulation for ionic liquids. I initially did simulation with Gromacs VERSION 4.0.7 with parrinello-rahman pressure coupling. Here I pasted temperature and pressure coupling part of mdp file. ; Temperature coupling is

Re: [gmx-users] PBC correction to visualize a protein-membrane structure

Dear Justin, thank you. I’ve tried the following but neither of them worked, I get the same result. trjconv -f input.gro -o output.gro -s .tpr -trans 0 0 z_box/2 -pbc mol -ur compact trjconv -f input.gro -o output.gro -s tpr -trans x_box/2 y_box/2 z_box/2 -pbc mol -ur compact This is

Re: [gmx-users] PBC correction to visualize a protein-membrane structure

On May 16, 2014 7:03 PM, Juan Munoz-Garcia juan.munoz-gar...@bioch.ox.ac.uk wrote: Dear Justin, thank you. I’ve tried the following but neither of them worked, I get the same result. trjconv -f input.gro -o output.gro -s .tpr -trans 0 0 z_box/2 -pbc mol -ur compact trjconv -f input.gro

Re: [gmx-users] berendsen vs parrinello-rahman

Unstable models or unstable initial conditions will behave unpredictably. Unfortunately you've not given us much to go on. Mark On May 16, 2014 6:08 PM, Nilesh Dhumal ndhu...@andrew.cmu.edu wrote: On 5/16/14, 11:37 AM, Nilesh Dhumal wrote: Hello, I am running the simulation for ionic

Re: [gmx-users] berendsen vs parrinello-rahman

One initial structure is equilibrated for 10ns using Gromacs VERSION 4.0.7. If I run same structure with same .mdp and same force field parameters using gromacs VERSION 4.5.5. I got the error system is blowing up. I made another new initial structure which is not equilibrated and I got the

[gmx-users] Questions about position restraint for charged proteins

Hello. I am currently using GROMACS4.6.5 and trying to simulate a fluorescent protein(GFP,1EMB.pdb) fused to a muscarinic acetylcholine receptor(M2,3UON.pdb). PDB file of M2(3UON.pdb) included a lysozyme part(res#1002-1161), so I removed it to make the simulation consistent with our

Re: [gmx-users] berendsen vs parrinello-rahman

What Michael said, and if your .mdp setup triggers a code path for which the implementation changed between 4.0.7 and 4.5.5 (like it did for at least twin-range), then you should see different behaviour. But I guess we'll have to keep making unproductive guesses. Mark On Fri, May 16, 2014 at

[gmx-users] mdrun error

Hi Everyone I need some help. With my mdrun command I am getting this following error . Program mdrun, VERSION 4.6.5 Source code file: /home/itlab/Documents/gromacs/gromacs-4.6.5/src/mdlib/domdec_con.c, line: 722 Fatal error: DD cell 0 0 1 could only obtain 1 of the 2 atoms that are