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
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Department of Pha
Where do I take that file from?
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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
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
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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?
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> 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 ?
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On Dec 4, 2013, at 3:06 PM, panzu wrote
> so How do I convert from .pdb to .gro the ?
Use editconf.
Carsten
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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 ?
>
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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
so How do I convert from .pdb to .gro?
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so How do I convert from .pdb to .gro the ?
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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
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 :
*
Thanks you all for the suggestions.
I wil try then...
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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
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.
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
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
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