I don't understand what you are asking for.
Mark
On May 17, 2013 7:59 AM, "Rasoul Nasiri" wrote:
> Are you sure lattice cell set up in f.c.c structure has been explained
> there for the positions of molecules?
>
>
>
>
> On Thu, May 16, 2013 at 3:28 PM, Mark Abraham >wrote:
>
> > Does manual 2.3
Are you sure lattice cell set up in f.c.c structure has been explained
there for the positions of molecules?
On Thu, May 16, 2013 at 3:28 PM, Mark Abraham wrote:
> Does manual 2.3 help?
>
>
> On Thu, May 16, 2013 at 2:51 PM, Rasoul Nasiri
> wrote:
>
> > Hi All,
> >
> > Has anyone performed MD
Does manual 2.3 help?
On Thu, May 16, 2013 at 2:51 PM, Rasoul Nasiri wrote:
> Hi All,
>
> Has anyone performed MD simulation on fluids in reduced units with GROMACS?
> I just wandering how the obtained density values through the box should be
> converted in the SI unit (Kg/m3).
>
> Thanks
> Ras
Hi All,
Has anyone performed MD simulation on fluids in reduced units with GROMACS?
I just wandering how the obtained density values through the box should be
converted in the SI unit (Kg/m3).
Thanks
Rasoul
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On 2/11/13 6:15 PM, Pengzhi Zhang wrote:
In my case, all the related units are about length, so I won't consider
temperature, charge etc.
Here is the confusion.
On one hand, from the above discussion: If the input is from the .pdb file,
which is in reduced units ( {\sigma}=3.8 Angstrom), as w
In my case, all the related units are about length, so I won't consider
temperature, charge etc.
Here is the confusion.
On one hand, from the above discussion: If the input is from the .pdb file,
which is in reduced units ( {\sigma}=3.8 Angstrom), as well as the
coordinate file, the program g_co
On 2/11/13 5:26 PM, Pengzhi Zhang wrote:
Justin, I'm a little confused again. Let me put it in a more general way. If
I used everything in .pdb and .trr files in reduced units {\sigma}, then
gromacs will assume them are in Angstroms, and output in nms (by dividing
the input values by 10). That
Justin, I'm a little confused again. Let me put it in a more general way. If
I used everything in .pdb and .trr files in reduced units {\sigma}, then
gromacs will assume them are in Angstroms, and output in nms (by dividing
the input values by 10). That means, the real unit for the output is
{\sigm
On 2/11/13 5:02 PM, Pengzhi Zhang wrote:
Thanks Justin.
I do use a .pdb file as the topology file, which is also in Angstrom, not in
full format of pdb though (basically atom index ,name and coordinates). So
in my case, gromacs will read all the coordinates in angstrom? Thus I need
to ignore t
Thanks Justin.
I do use a .pdb file as the topology file, which is also in Angstrom, not in
full format of pdb though (basically atom index ,name and coordinates). So
in my case, gromacs will read all the coordinates in angstrom? Thus I need
to ignore the units nm in output .xvg files. Do I unders
On 2/11/13 4:09 PM, Pengzhi Zhang wrote:
Hello there,
I'm a gromacs newbie. I am using gromacs function g_anaeig to do principle
component analysis. I use coordinates (converted to be .trr files for
gromacs) and topology from amber. I know that gromacs works with units like
nm, kJ/mol etc, whi
Hello there,
I'm a gromacs newbie. I am using gromacs function g_anaeig to do principle
component analysis. I use coordinates (converted to be .trr files for
gromacs) and topology from amber. I know that gromacs works with units like
nm, kJ/mol etc, while amber with angstrom. Does anyone know tha
Dear all
I would like to do coarse-grained simulations using reduced LJ units. As I
can see in the manual, this is possible, but I don't understand how...
I use the Gromos96 53a6 force field.
In the *ffG53a6nb.itp *the* σ* and *ε* are in *(nm*) and *(KJ/mol*)
Also in the *ffG53a6.atp* the *mas*s
On Mon, Aug 9, 2010 at 9:58 AM, wrote:
> Hi,
>
> I want to use the pme algorithm in GROMACS. Thge size of my box is
> 8.2x8.2x8.2 in reduced units. I am considering a collection of 1000
> of CO2 molecules. If I am using reduced units, the values of the
> parameters "rcoulomb=0.9" I think should b
Hi,
I want to use the pme algorithm in GROMACS. Thge size of my box is
8.2x8.2x8.2 in reduced units. I am considering a collection of 1000
of CO2 molecules. If I am using reduced units, the values of the
parameters "rcoulomb=0.9" I think should be converted to reduced
units "rcoulomb=2.45" (my \si
On Sat, Oct 17, 2009 at 06:10, lammps lammps wrote:
> Dear,
>
> I want to do stochastic simulations in the framework of Langevin dynamics
> using Gromacs with the reduced units. The questions are:
>
> 1. How to turn on the reduced units? Is there any parameters for setting?
>
> I am not sure I u
Dear,
I want to do stochastic simulations in the framework of Langevin dynamics
using Gromacs with the reduced units. The questions are:
1. How to turn on the reduced units? Is there any parameters for setting?
2. If I use the reduced temperature of 1, should the ref_t in the .mdp file
be the 1
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