[gmx-users] problem with NVT equilibration

2012-02-13 Thread Anushree Tripathi
Shall we use 'residuetypes.dat' file in 'grompp -f minim.mdp -c system_solv_ions.gro -p topol.top -o em.tpr' command without creating index file? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.

Re: [gmx-users] problem with nvt equilibration

2012-02-06 Thread Mark Abraham
On 6/02/2012 11:09 PM, Anushree Tripathi wrote: Will you please send me the basic tutorial in which I can find how to use -n option in " grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr" command. All the tutorials provide examples of using the general syntax command -x value -y file.ext f

Re: [gmx-users] problem with nvt equilibration

2012-02-06 Thread Anushree Tripathi
Will you please send me the basic tutorial in which I can find how to use -n option in " grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr" command. On Mon, Feb 6, 2012 at 5:17 PM, Justin A. Lemkul wrote: > > > Anushree Tripathi wrote: > >> where should I use -n option in the command (i.e., gr

Re: [gmx-users] problem with nvt equilibration

2012-02-06 Thread Justin A. Lemkul
Anushree Tripathi wrote: where should I use -n option in the command (i.e., grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr).Please tell me. I would suggest you refer to grompp -h and/or go through some basic tutorial material so that you can get a feel for command line options and how

Re: [gmx-users] problem with nvt equilibration

2012-02-06 Thread Anushree Tripathi
where should I use -n option in the command (i.e., grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr).Please tell me. On Mon, Feb 6, 2012 at 4:58 PM, Mark Abraham wrote: > On 6/02/2012 8:28 PM, Anushree Tripathi wrote: > >> Inspite of having DPPC in index file,when I run the command ( i.e., >>

Re: [gmx-users] problem with nvt equilibration

2012-02-06 Thread Mark Abraham
On 6/02/2012 8:28 PM, Anushree Tripathi wrote: Inspite of having DPPC in index file,when I run the command ( i.e., grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr ),I am getting the error: Group DPPC not found in indexfile. Maybe you have non-default goups in your .mdp file, while not usin

[gmx-users] problem with nvt equilibration

2012-02-06 Thread Anushree Tripathi
Inspite of having DPPC in index file,when I run the command ( i.e., grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr ),I am getting the error: Group DPPC not found in indexfile. Maybe you have non-default goups in your .mdp file, while not using the '-n' option of grompp. In that case use the '