[gmx-users] Md simulation mdp options error

Hi, I am trying to run a simulation with the following optins in my production mdp file. Previously I have run the simulations with the production run parameters using V-rescale thermostat and berendsen barostat. But now recently I read in discussion that Justin had advised using Parinello-Rahman

Re: [gmx-users] Md simulation mdp options error

On 4/18/14, 4:57 AM, Ankita Naithani wrote: Hi, I am trying to run a simulation with the following optins in my production mdp file. Previously I have run the simulations with the production run parameters using V-rescale thermostat and berendsen barostat. But now recently I read in

Re: [gmx-users] Md simulation mdp options error

Thank you Justin for your reply. Yes indeed this is a production run. So would the following mdp file be okay now? title= production MD ; Run parameters integrator= md; leap-frog algorithm nsteps= 5000; 0.002 * 5000 = 10 ps or 100 ns dt =

Re: [gmx-users] Md simulation mdp options error

On 4/18/14, 8:55 AM, Ankita Naithani wrote: Thank you Justin for your reply. Yes indeed this is a production run. So would the following mdp file be okay now? title= production MD ; Run parameters integrator= md; leap-frog algorithm nsteps= 5000; 0.002 *

Re: [gmx-users] Md simulation mdp options error

Also, just one more floating query... In presssure coupling, Previously, I have been using tau_p = 1.0 but for this simulaion, I have changed it to tau_p = 2.0 This was after seeing the mdp file of one of your tutorials. Just wanted to confirm if that's okay. -- Gromacs Users mailing list *

Re: [gmx-users] pdb2gmx yielding (a couple of) -nan values for coordinates of built hydrogen atoms

Excellent blind diagnosis Mark! VMD molefacture seems to build leucines with nearly linear CA-CB-CG angles. In one case I got an angle that was exactly linear, hence the problem for pdb2gmx to build the hydrogens. I'll report to VMD; I'll also file an enhancement request for pdb2gmx to provide

[gmx-users] Dipole moment calculations

Hello, How does Gromacs calculate the dipole moment? Does it calculate the distance of a atom from origin (0.0,0.0,0.0) or distance from center of box (box_length/2, box_length/2, box_length/2) Nilesh -- Gromacs Users mailing list * Please search the archive at

[gmx-users] How to explain the phenomenon of -genbox?

Hi, I use : genbox -cp box.6_newbox.gro -cs spc216.gro -o box.6_solv.pdb -p box.6.top Output configuration contains 301821 atoms in 100053 residues Volume : 3030.92 (nm^3) Density: 1000.12 (g/l) Number of SOL molecules: 99801 When I use VMD to see the

[gmx-users] mpirun error

Hi, I use grompp -f nvt.mdp -c em.gro -p box.6.top -o nvt.tpr mpirun -np 8 mdrun_mpi -deffnm nvt and get NOTE: The number of threads is not equal to the number of (logical) cores and the -pin option is set to auto: will not pin thread to cores.

Re: [gmx-users] mpirun error

On 4/18/14, 6:53 PM, maggin wrote: Hi, I use grompp -f nvt.mdp -c em.gro -p box.6.top -o nvt.tpr mpirun -np 8 mdrun_mpi -deffnm nvt and get NOTE: The number of threads is not equal to the number of (logical) cores and the -pin option is set to auto:

Re: [gmx-users] mpirun error

Hi, Justin Ya, multiple jobs are using the same set of nodes, so I try it as: mpirun -np 8 mdrun_mpi -deffnm nvt -pin off it ok! I find multiple jobs are using the same set of nodes, they run slower. If I use -pin off, it will run normal, is it right? Thank you very much! maggin -- View

Re: [gmx-users] mpirun error

On 4/18/14, 7:45 PM, maggin wrote: Hi, Justin Ya, multiple jobs are using the same set of nodes, so I try it as: mpirun -np 8 mdrun_mpi -deffnm nvt -pin off it ok! I find multiple jobs are using the same set of nodes, they run slower. If I use -pin off, it will run normal, is it right?

Re: [gmx-users] How to explain the phenomenon of -genbox?

at the step: editconf -f box.6.gro -o box.6_newbox.gro -c -d 1 -bt cubic box.6_newbox.gro is right, no problem; following, I use: genbox -cp box.6_newbox.gro -cs spc216.gro -o box.6_solv.pdb -p box.6.top so, this strange happen. While at NVT step, it looks ok. the nvt.gto is:

[gmx-users] Reproducibility in free energy calculations.

Hello Justin, I tried the free energy calculations in your tutorial at different sets of conditions. Also I repeated a simulation at the same conditions with same parameters, thrice on the same computer on same number of processors. The results in the three cases where different (4.16 +/- 0.19