[gmx-users] Can't do GB electrostatics; the implicit_genborn_params section of the forcefield is missing parameters for

Dear gmx-users: When I try to simulation a system: protein + ligand molecule using the Implicit Solvent method. the parameters of Ligand were produced by acpype, but when grompped, the appeared" " Velocities were taken from a Maxwell distribution at 300 K GB parameter(s) missing or negative for

Re: [gmx-users] Can't do GB electrostatics; the implicit_genborn_params section of the forcefield is missing parameters for

On 2/06/2012 7:10 PM, xi zhao wrote: Dear gmx-users: When I try to simulation a system: protein + ligand molecule using the Implicit Solvent method. the parameters of Ligand were produced by acpype, but when grompped, the appeared" " Velocities were taken from a Maxwell distribution at 300 K G

[gmx-users] About extend the run,,

Hi Gromacs Friends, I run a Production run with saving the co-ordinates and velocity after every 500 steps for 20ns.. Now I want to extend the run but with saving the co-ordinates and velocity after every 1000 steps for next 30ns (total 50ns) To perform these task I am using following command 1

Re: [gmx-users] About extend the run,,

On 6/2/12 10:27 AM, rama david wrote: Hi Gromacs Friends, I run a Production run with saving the co-ordinates and velocity after every 500 steps for 20ns.. Now I want to extend the run but with saving the co-ordinates and velocity after every 1000 steps for next 30ns (total 50ns) To perform

[gmx-users] How to prevent box shrinking incessantly at x and y when doing membrane simulation using semiisotropic couple type?

I suspect that you can find an equation to relate the surface tension to the ratio of the pressure along z to the pressure along xy that is required to maintain the unit cell of a semi-isotropic simulation approximately constant when you use the same compressibility in all dimensions. You might

Re: [gmx-users] About extend the run,,

Thank you Justin for quick reply On Sat, Jun 2, 2012 at 8:12 PM, Justin A. Lemkul wrote: > > > To perform these task I am using following command >> 1. grompp -f -t <.cpt> -c >> <.gro >> file(gro file from position restrained run )> -o new.tpr >> >> >> 2. tpbconv -s new.tpr -0 extend.tp

Re: [gmx-users] About extend the run,,

On 6/2/12 11:23 AM, rama david wrote: Thank you Justin for quick reply On Sat, Jun 2, 2012 at 8:12 PM, Justin A. Lemkul mailto:jalem...@vt.edu>> wrote: To perform these task I am using following command 1. grompp -f -t <.cpt> -c <.gro file(gro file fr

[gmx-users] how to run production MD for only a fragment of protein

Dear All,   Can you tell me a web link on a protocol or reference for steered production MD or the production MD just for only a fragment of the whole protein, by GROMACS?   Cheers,   Acoot-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Pleas

Re: [gmx-users] how to run production MD for only a fragment of protein

On 6/2/12 11:33 AM, Acoot Brett wrote: Dear All, Can you tell me a web link on a protocol or reference for steered production MD or the production MD just for only a fragment of the whole protein, by GROMACS? That's sort of a broad request. If you can describe more specifically what you wan

Re: [gmx-users] About extend the run,,

Thank You for Quick reply Justin... On Sat, Jun 2, 2012 at 8:58 PM, Justin A. Lemkul wrote: > > You'll get a mismatch in your files (checkpoint, trajectory, energy) in > terms of frame interval. You should not try to append to these files or > extend the run. Just run a new simulation from 2

[gmx-users] Calculate surface tension

Dear Gromacs Users, I am trying to calculate the surface tension at air/water interface of water model SPC/E. I used the command g_energy and chose #surfacetension. However, the output file was like this: 0 14001.49219 0.5 21139.67773 1 7328.798828 1.5 16114.55664 2 8224.392578 2.5 16558.3