[gmx-users] Stop protein diffusion in simulation box to make a movie

Dear Gromacs Users, I made a trajectory movie using VMD and smoothing increased for getting the residues motion slower, but the protein is translate and diffuse in box, and causes very hard of seeing and analyzing how ligand structure changes during simulation. How can I stop the protein

Re: [gmx-users] Stop protein diffusion in simulation box to make a movie

hi. can this help? http://manual.gromacs.org/programs/gmx-trjconv.html On Sat, Dec 13, 2014 at 6:04 AM, Hassan Aaryapour hassan.grom...@gmail.com wrote: Dear Gromacs Users, I made a trajectory movie using VMD and smoothing increased for getting the residues motion slower, but the protein is

Re: [gmx-users] adding hydrogen atoms into a POPC membrane

On 12/13/14 12:47 AM, Carlos Navarro Retamal wrote: Dear gromacs users, I just ran a CG simulation of a system consisting in a protein embedded in a POPC membrane solvated in water. After that i ran the script .initram to obtain an AA representation of my system (gromos54a7), but sadly i

Re: [gmx-users] adding hydrogen atoms into a POPC membrane

Hey, The all atom mapping of Martini to CHARMM36 is available in backward/initram, so the conversion can be done directly. You only need to have a CHARMM36 POPC itp file. I can provide one if needed. Cheers, Tsjerk On Dec 13, 2014 3:38 PM, Justin Lemkul jalem...@vt.edu wrote: On 12/13/14

Re: [gmx-users] Maximun time-step recommended in the grompp part for each system

Some extra information about this topic: We are exicitely interested in NOT using any kind of constraints. As you may assume, the purpose of this study is purely theoretical. Thank you very much. Best regards, Mario El 11/12/2014 18:20, Mario Fernández Pendás mariof...@gmail.com escribió:

[gmx-users] Need to Sort Out

I am facing a problem in Gromacs while running grommp please do give the right direction I am new to Molecular dynamics. Fatal error: Syntax error - File topol_Protein_chain_A.itp, line 6966 Last line read: '[ molecules ]' Invalid order for directive molecules For more information and tips for

Re: [gmx-users] Need to Sort Out

Hi. I'm quite new to molecular dynamics too. How did you make that itp? Does your system contain only one protein/DNA molecule? May be try this tutorial for a single protein? http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/ Check multiple journal papers when you

[gmx-users] Is the discontinuity in type 2 improper dihedrals at 90 deg. or 180 deg. ?

Dear Users: In gromacs, the charmm27 force field uses type 2 (non-periodic) improper dihedrals to maintain planarity of peptide bonds. Type 2 dihedrals are described on page 70 of the 4.6.7 manual and page 80 of the 5.0.2 manual, which contain the line (identical text): Since the potential is

[gmx-users] content of trr / xtc files + -b/-e flag question + tpr question

Hello Gromacs users. I have a few questions. I ran two small trajectories: trajectory 1: dt = 0.0008 nsteps=10 nstxout=2 nstxtcout=3 trajectory 2: dt = 0.0008 nsteps=10 nstxout=3 nstxtcout=2 We can examine the content of each trajectory using trajconv -sep -nzeros 1. The initial frame is