Re: [gmx-users] Atomistic Simulation

2013-12-05 Thread Justin Lemkul
On 12/5/13 4:39 AM, panzu wrote: Where do I take that file from? The standard force field files located in $GMXLIB. Consult the manual and/or any basic tutorial. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pha

Re: [gmx-users] Atomistic Simulation

2013-12-05 Thread panzu
Where do I take that file from? -- View this message in context: http://gromacs.5086.x6.nabble.com/Atomistic-Simulation-tp5012984p5013092.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.

Re: [gmx-users] Atomistic Simulation

2013-12-04 Thread Justin Lemkul
On 12/4/13 9:50 AM, panzu wrote: The thing is when I tray to use the grompp comand: bash >> g_grompp -f grompp.mdp -c tolu.pdb -p topol.top Back Off! I just backed up mdout.mdp to ./#mdout.mdp.5# NOTE 1 [file grompp.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setti

Re: [gmx-users] Atomistic Simulation

2013-12-04 Thread panzu
The thing is when I tray to use the grompp comand: bash >> g_grompp -f grompp.mdp -c tolu.pdb -p topol.top Back Off! I just backed up mdout.mdp to ./#mdout.mdp.5# NOTE 1 [file grompp.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting nstcomm to nstcalcenergy --

Re: [gmx-users] Atomistic Simulation

2013-12-04 Thread Hardy, Adam
You don't need to. Gromacs accepts pdb, gro and several other coordinate file formats. On 4 Dec 2013 14:30, panzu wrote: so How do I convert from .pdb to .gro? -- View this message in context: http://gromacs.5086.x6.nabble.com/Atomistic-Simulation-tp5012984p5013059.html Sent from the GROMACS

Re: [gmx-users] Atomistic Simulation

2013-12-04 Thread Ricardo O. S. Soares
s.org > Enviadas: Quarta-feira, 4 de Dezembro de 2013 12:06:28 > Assunto: Re: [gmx-users] Atomistic Simulation > so How do I convert from .pdb to .gro the ? > -- > View this message in context: > http://gromacs.5086.x6.nabble.com/Atomistic-Simulation-tp5012984p5013058.html > Sent

Re: [gmx-users] Atomistic Simulation

2013-12-04 Thread Carsten Kutzner
On Dec 4, 2013, at 3:06 PM, panzu wrote > so How do I convert from .pdb to .gro the ? Use editconf. Carsten -- 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/Sup

Re: [gmx-users] Atomistic Simulation

2013-12-04 Thread jkrieger
You don't need to. Later processing steps such as editconf, genbox and grompp can read .pdb files. > so How do I convert from .pdb to .gro the ? > > -- > View this message in context: > http://gromacs.5086.x6.nabble.com/Atomistic-Simulation-tp5012984p5013058.html > Sent from the GROMACS Users Foru

Re: [gmx-users] Atomistic Simulation

2013-12-04 Thread Justin Lemkul
On 12/4/13 9:06 AM, panzu wrote: so How do I convert from .pdb to .gro the ? You don't technically need one: http://www.gromacs.org/Documentation/File_Formats/Coordinate_File If you prefer to use .gro format, just convert with editconf. The job of pdb2gmx is to produce a topology; the ou

Re: [gmx-users] Atomistic Simulation

2013-12-04 Thread panzu
so How do I convert from .pdb to .gro? -- View this message in context: http://gromacs.5086.x6.nabble.com/Atomistic-Simulation-tp5012984p5013059.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Gromacs Users mailing list * Please search the archive at http://www.

Re: [gmx-users] Atomistic Simulation

2013-12-04 Thread panzu
so How do I convert from .pdb to .gro the ? -- View this message in context: http://gromacs.5086.x6.nabble.com/Atomistic-Simulation-tp5012984p5013058.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Gromacs Users mailing list * Please search the archive at http://w

Re: [gmx-users] Atomistic Simulation

2013-12-04 Thread Justin Lemkul
On 12/4/13 6:15 AM, panzu wrote: Hello users, After downloading the toluene.pdb file of a toluene molecule and its forcefield tolu.itp from "Automated Topology Builder" and saved in the root /usr/share/gromacs/top/gromos53a6.ff I use the next comand i order to convert the pdb format to .gro

Re: [gmx-users] Atomistic Simulation

2013-12-04 Thread panzu
Hello users, After downloading the toluene.pdb file of a toluene molecule and its forcefield tolu.itp from "Automated Topology Builder" and saved in the root /usr/share/gromacs/top/gromos53a6.ff I use the next comand i order to convert the pdb format to .gro : *

Re: [gmx-users] Atomistic Simulation

2013-12-04 Thread panzu
Thanks you all for the suggestions. I wil try then... -- View this message in context: http://gromacs.5086.x6.nabble.com/Atomistic-Simulation-tp5012984p5013039.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Gromacs Users mailing list * Please search the archive a

Re: [gmx-users] Atomistic Simulation

2013-12-03 Thread lloyd riggs
anged, but you may not notice it until short simulations are run, with all other atoms out of 30-40 correct...).   Stephan Watkins   Gesendet: Dienstag, 03. Dezember 2013 um 12:17 Uhr Von: "Hardy, Adam" An: "gmx-us...@gromacs.org" Betreff: Re: [gmx-users] Atomistic Simulation

Re: [gmx-users] Atomistic Simulation

2013-12-03 Thread Justin Lemkul
On 12/3/13 6:17 AM, Hardy, Adam wrote: I've just started doing atomistic simulations over the last few weeks as well and can share what I've learned so far. I have been using 'automated topology builder'. It only uses the gromos 53a6 forcefield so eliminates the choice if you want to use it.

Re: [gmx-users] Atomistic Simulation

2013-12-03 Thread Hardy, Adam
I've just started doing atomistic simulations over the last few weeks as well and can share what I've learned so far. I have been using 'automated topology builder'. It only uses the gromos 53a6 forcefield so eliminates the choice if you want to use it. ATB generates the pdb and itp files for y

[gmx-users] Atomistic Simulation

2013-12-03 Thread panzu
Hello to everybody, I am new in atomistic simulations and a have some doubts about how to do it. I wanna simulate a mixture of Cyclohexane, Toluene and Dodecane. My questions are, ¿Where do I get the pdb files of these molecules from? and ¿How do I know which force field I should choose in p