Re: [gmx-users] [gmx-developers] How to put two molecules inside the simulation box with a control on their DISTANCE and ANGLE

GROMACS Users emailing list more appropriate for this question. You can used editconf to translate, rotate coordinates around. So move the 2nd one around, then copy / paste the coordinates into the 1st coordinate file, making sure adjust the atom number count and maintain the correct

Re: [gmx-users] KALP 15 in model membrane

Hi, Putting capping on the peptide/protein end affect the its polarity and you should check how it could affect your protein structure or whether you want it to be charged or not at the tails. Cheers, Armin On Mon, Feb 12, 2018 at 9:39 PM, Negar Parvizi wrote: > Dear

Re: [gmx-users] tune_pme error with GROMACS 2018

Carsten, I was hoping yo use tune_pme to optimize a REMD job across multiple nodes, so I think I need it compiled with MPI (please let me know if that logic is incorrect). I am indeed running on GPU nodes (I tested mdrun on the nodes and and there was no issue). Best, Dan On Mon, Feb 12, 2018

[gmx-users] charmm36 force field

Dear GMX users I used charmm36 force field to run MD simulation on my receptor and ligand which has 2 phosphotyrosine groups. All of steps that I did are following as: 1) gmx pdb2gmx -f .pdb -o .gro -water tip4p -ignh -his2) gmx editconf -f .gro -o newbox.gro -c -d 1.0 -bt dodecahedron3)gmx

[gmx-users] Parallelization in large system

Dear Gromacs users, I am trying to simulate a large system (roughly 3M atoms including solvent) on Gromacs version 4.5.5. I am having difficulty having mdrun execute parallel calculations. I have run several variations (described below) of attempting steepest descent minimization and the

[gmx-users] Solvation energy estimation gmx sasa

Hi, I'd like to ask about solvation energy given in gmx sasa (gromacs 2016) with option: -odg What algorithm is used here, or rather - what values are given for area of particular atom types? I guess there is publication behind this, but the only mentioned in gmx sasa focus on solvation area. Is

[gmx-users] how can i restrain Zn ion during simulations

Dear gromacs users, I am currently running simulations for protein-RNA complex. However i have to include one Zn ion which is coordinated by 4 cysteine residues. when i performed energy minimization itself zinc displaces. How can i restrain to Zn, or to freeze Zn during simulations. Thanks in

Re: [gmx-users] REMD DLB bug

Hi, The fix will be released in an upcoming 2016.5 patch release. (which you can see in the redmine issue page "Target version" field BTW). Cheers, -- Szilárd On Mon, Feb 12, 2018 at 2:49 PM, Akshay wrote: > Hello All, > > I was running REMD simulations on Gromacs

[gmx-users] REMD DLB bug

Hello All, I was running REMD simulations on Gromacs 2016.1 when my simulation crashed with the error Assertion failed: Condition: comm->cycl_n[ddCyclStep] > 0 When we turned on DLB, we should have measured cycles I saw that there was a bug #2298 reported about this recently at

[gmx-users] PBC

Hi If I want to use gmx trjconv to recenter the protein in xtc file, the reference (-s) .tpr should be the one I used in simulation (md.tpr) or I can use the first one (em.tpr) without a difference? This is because the protein has jumped after em step, and if I have to use md.tpr as reference

Re: [gmx-users] tune_pme error with GROMACS 2018

Hi Dan, > On 11. Feb 2018, at 20:13, Daniel Kozuch wrote: > > Hello, > > I was recently trying to use the tune_pme tool with GROMACS 2018 with the > following command: > > gmx tune_pme -np 84 -s my_tpr.tpr -mdrun 'gmx mdrun’ Maybe you need to compile gmx without MPI (so

Re: [gmx-users] Fwd: MMPBSA

On Fri, Feb 9, 2018 at 8:14 AM, RAHUL SURESH wrote: > Dear all > > I have carried out a protein ligand simulation for 50ns and performed a > PBSA calculation for 10-20ns trajectory. I get a positive binding energy. > How can I tackle it..? > > Thank you > > I think you

Re: [gmx-users] Tests with Threadripper and dual gpu setup

BS”D Did you build with or without hwloc? I did use hwloc. — Gromacs 2018 rc1 (using gcc 4.8.5) — Using AVX_256 You should be using AVX2_128 or AVX2_256 or Zen! The former will be fastest in CPU-only runs, the latter can often be (a bit) faster in GPU

[gmx-users] Prolactin receptor in a mixed DPPC-DMPC bilayer

Dear all Gromacs users, I want to simulate prolactin receptor in a mixed DPPC-DMPC bilayer. At first, I will insert the trans membrane part of the protein (prolactin receptor) in the bilayer and do the necessary modifications to the FF, according to the Justin,s membrane protein tutorial. It

[gmx-users] KALP 15 in model membrane

Dear all Gromacs usersI have started the tutorial on membrane protein, provided by Justin ( KALP 15 in model membrane).Now I have two questions:1) Why Justin adds the ACE and NH2 groups to the two ends of the peptide model? The -ter option in pdb2 gmx command can add interactively the NH2 or

Re: [gmx-users] pressure coupling error in umbrella sampling

Hi Dr.Abraham Thank you very much for your answer yas I ve extacted configuration with 0.2 nm distance and when I want to run NPT for first configuration,I gave that error. I didnt undersatnd this mdp file for this step, I got this file from umbrella sampling tutorial and I adjusted for my