Re: [gmx-users] Number of ligand contacts over the trajectories

g_mindist with -on and -d option. On Mon, Oct 14, 2013 at 11:37 AM, anu chandra wrote: > Dear Gromacs users, > > I am working with protein-ligand interaction. I would like to calculate the > number of contacts ligand make with the protein within a specific cut off ( > say within 3.5 to 4.5 angs

[gmx-users] KALP in DPPC tutorial reg

Hi, I'm doing the KALP-15 IN DPPC through the Justin's tutorial http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/03_solvate.html After generating the new position restrain file, I start to energy minimization to get the correct area per lipid. As below: Sc

[gmx-users] Re: Steered MD

First of all, sorry for the late answer. More generally it is said the the rupture force depends logarithmically on the loading rate (velocity times spring constant). -> So the rup.force should also depend logarithmically on the spring constant (in the simple bell modell). Think the reason, wh

Re: [gmx-users] DSSP problem

On 10/13/13 11:56 PM, Mass wrote: Hi Justin Here is the copied and pasted output Mass@Mass-ThinkPad-Edge-E530:~/bLac_run_simulations_200ns_analyzed/original$ ls -l -rw--- 1 Mass Mass 15351454992 Aug 21 07:51 bLac_orig_md2.trr Try giving readable permissions to all, i.e. chmod +r. Wit

Re: [gmx-users] KALP in DPPC tutorial reg

On 10/14/13 2:44 AM, Sathya wrote: Hi, I'm doing the KALP-15 IN DPPC through the Justin's tutorial http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/03_solvate.html After generating the new position restrain file, I start to energy minimization to get the

[gmx-users] g_sham

Dear all gromacs users I am creating free energy landscape using g_sham but my axis are not getting labelled. I have searched the archive and found that using xmin and xmax options we can label them. I have first created my 2D projection xvg file using g_anaeig -f *.xtc -s *.tpr -first 1 -last 2 -

Re: [gmx-users] g_sham

On 10/14/13 7:54 AM, pratibha kapoor wrote: Dear all gromacs users I am creating free energy landscape using g_sham but my axis are not getting labelled. I have searched the archive and found that using xmin and xmax options we can label them. I have first created my 2D projection xvg file usi

[gmx-users] Wall option with 12-6 LJ

Dear all, I am trying to apply wall options using 12-6 LJ potential. Right now I am using isotropic Berendsen pressure coupling, my first question is, is that the correct method? When I tried to use semi isotropic pressure coupling, the box dramatically expanded. And below is the simulation o

[gmx-users] problem in NPT equilibration step

Dear Gromacs user, I am trying to simulate a protein (nmr structure).I have successfully done energy minimisation step.Also I have equilibrated the system a 298 k (which is achieved from 100 ps run) .Now,I am trying to equilibrate the system at 1 bar pressure.After a run of 100 ps ,I am getting av

Re: [gmx-users] problem in NPT equilibration step

Hi, Parrinello-Rahman coupling usually allows wide fluctuations in the pressure. I would suggest to take Berendsen algorithm for equilibrating your system, and then extend the simulation with PR if you need to. Bests, baptiste 2013/10/14 Preeti Choudhary > Dear Gromacs user, > > I am trying

Re: [gmx-users] problem in NPT equilibration step

The barostat tries to equilibrate the system at the desired pressure, there will be fluctuations and these fluctuations are little higher for Parrinello-rahman if started far away from equilibrium value. I would suggest to start from berendsen and then extend it to P-R. Also, you should run little

Re: [gmx-users] problem in NPT equilibration step

http://www.gromacs.org/Documentation/Terminology/Pressure_Coupling and http://www.gromacs.org/Documentation/Terminology/Pressure are useful here. Mark On Mon, Oct 14, 2013 at 4:32 PM, srinathchowdary wrote: > The barostat tries to equilibrate the system at the desired pressure, there > will be

[gmx-users] LJ - SR and Coulbom - SR mdp options

Dear Gmx Users, I want to obtain average Protein-Ligand SR electrostatics and LJ energy values using g_energy from NPT equlibration with position restraints. I used energygrps = Protein LIG However, when I run g_energy -f npt.edr -s npt.tpr I see neither Protein-LIG for any of them. Would you pl

[gmx-users] recalculating .trr from .xtc

Dear GROMACS users, Does anyone know how significant is the difference between the "original" .trr file from a simulation and a "recalculated" .trr from a whole system .xtc (mdrun -rerun traj.xtc -o traj.trr)? I mean... do you know how big would be the error induced by this "recalculatio

Re: [gmx-users] LJ - SR and Coulbom - SR mdp options

On 10/14/13 2:03 PM, Steven Neumann wrote: Dear Gmx Users, I want to obtain average Protein-Ligand SR electrostatics and LJ energy values using g_energy from NPT equlibration with position restraints. I used energygrps = Protein LIG However, when I run g_energy -f npt.edr -s npt.tpr I see ne

Re: [gmx-users] recalculating .trr from .xtc

On 10/14/13 7:56 PM, Leandro Bortot wrote: Dear GROMACS users, Does anyone know how significant is the difference between the "original" .trr file from a simulation and a "recalculated" .trr from a whole system .xtc (mdrun -rerun traj.xtc -o traj.trr)? I mean... do you know how big

Re: [gmx-users] recalculating .trr from .xtc

Also, the precision was selected when the xtc file was written, ie in the mdp file. Mark On Oct 15, 2013 3:24 AM, "Justin Lemkul" wrote: > > > On 10/14/13 7:56 PM, Leandro Bortot wrote: > >> Dear GROMACS users, >> >> Does anyone know how significant is the difference between the >> "origin