[gmx-users] I have not been able to do dPCA

Dear gromacs users, I would like to do dihedral PCA for my 20 residues trajectory. As I have interested in first 10 residues of my peptide, I have generated the .ndx file which has the dihedral atoms of first ten residues. Then I executed the following command. gmx_mpi angle -f md_0_1.xtc -s md_

[gmx-users] Simulation crashed

Hi All, I am doing CG simulation on lipid monolayer with gold nanoparticles (AuNP). I have done the simulation with single 3nm AuNP and two lipid monolayers apart by 6nm water slab. The NP was placed 6nm above from the upper monolayer. This system is also fine with 3NPs. I have an another system

[gmx-users] some thoughts on gmx wham

This is probably for Justin once again... My understanding is that you plan to work on a new tutorial for PMF calculations, so may be this could be useful. I recall asking you about selection of k and the corresponding spacing between configurations. We agreed that there is no strict way of setting

Re: [gmx-users] Protein-protein complex regarding

On 4/30/18 4:48 PM, RAHUL SURESH wrote: Dear all I am doing MD simulation of a Protein protein complex docked using Zdock server in charmm36 ff. Is it mandatory to treat a protein like a ligand as in protein-ligand tutorial and apply position constraint? Or is it fine if I simply simulate the

[gmx-users] Protein-protein complex regarding

Dear all I am doing MD simulation of a Protein protein complex docked using Zdock server in charmm36 ff. Is it mandatory to treat a protein like a ligand as in protein-ligand tutorial and apply position constraint? Or is it fine if I simply simulate the complex in solvent without adding any extra

Re: [gmx-users] strange GPU load distribution

Hi Mark, We checked and one example is below. Thanks, Alex PID TTY  STAT   TIME COMMAND 60432 pts/8    Dl+ 0:01 gmx mdrun -table ../../../tab_it.xvg -nt 1 -nb cpu -pme cpu -deffnm em_steep On 4/27/2018 2:16 PM, Mark Abraham wrote: Hi, What you think was run isn't nearly as useful w

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 167, Issue 139

Thanks for helping out. Have tried this it works fine I hope. On Wed, Mar 28, 2018 at 12:45 PM, < gromacs.org_gmx-users-requ...@maillist.sys.kth.se> wrote: > Send gromacs.org_gmx-users mailing list submissions to > gromacs.org_gmx-users@maillist.sys.kth.se > > To subscribe or unsubscribe

Re: [gmx-users] Heme topology

On 4/30/18 1:18 AM, Ragothaman Yennamalli wrote: We have a heme for which PRODRG does not generate the topology file, as Fe atom is not supported. Is there an alternative for generating topology file for Heme molecule? GROMOS and CHARMM force fields support heme without any additional param