Re: [gmx-users] dimensions of the box

On 1/10/18 12:56 PM, RAHUL SURESH wrote: Dear Justin I would like to add here something that is happening in my gromacs simulation. I am trying to extend timulation to another 50ns. commands as follows gmx convert-tpr -s alz.tpr -extend 5 -o extend.tpr gmx mdrun -v -deffnm extend -gpu_id

Re: [gmx-users] dimensions of the box

Dear Justin I would like to add here something that is happening in my gromacs simulation. I am trying to extend timulation to another 50ns. commands as follows gmx convert-tpr -s alz.tpr -extend 5 -o extend.tpr gmx mdrun -v -deffnm extend -gpu_id 00 -nt 4 it shows 15 days for the simulatio

Re: [gmx-users] dimensions of the box

Thank you all On Tue, 9 Jan 2018 at 6:33 PM, Justin Lemkul wrote: > > > On 1/8/18 6:18 AM, RAHUL SURESH wrote: > > Dear all > > > > For a protein-ligand simulation, > > > > for the command > > > > gmx editconf -f complex.gro -o newbox.gro -bt cubic -d 1.0 -c > > > > Read 680 atoms > > Volume: 25

Re: [gmx-users] dimensions of the box

On 1/8/18 6:18 AM, RAHUL SURESH wrote: Dear all For a protein-ligand simulation, for the command gmx editconf -f complex.gro -o newbox.gro -bt cubic -d 1.0 -c Read 680 atoms Volume: 25.6402 nm^3, corresponds to roughly 11500 electrons No velocities found system size : 3.411 17.359 3.

Re: [gmx-users] dimensions of the box

You can manually design the box, see gmx editconf -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://

[gmx-users] dimensions of the box

Dear all For a protein-ligand simulation, for the command gmx editconf -f complex.gro -o newbox.gro -bt cubic -d 1.0 -c Read 680 atoms Volume: 25.6402 nm^3, corresponds to roughly 11500 electrons No velocities found system size : 3.411 17.359 3.004 (nm) diameter: 17.543