Thank you!!
On Mon, Feb 11, 2013 at 8:29 PM, Justin Lemkul wrote:
>
>
> On 2/11/13 9:16 PM, ram bio wrote:
>>
>> Hi Justin,
>>
>> Thanks for the suggestion.
>>
>> I executed the following command:
>>
>> g_dist -f n101c2naclprod2-12nsvrpr.trr -s
>> n101c2naclpose2prod2nsvrpr.tpr -n index.ndx -dist
On 2/11/13 9:16 PM, ram bio wrote:
Hi Justin,
Thanks for the suggestion.
I executed the following command:
g_dist -f n101c2naclprod2-12nsvrpr.trr -s
n101c2naclpose2prod2nsvrpr.tpr -n index.ndx -dist 0.35 -o
N101Cbest2NACL606S336HG1.xvg
and the output was distance calculated for every 10 fr
Hi Justin,
Thanks for the suggestion.
I executed the following command:
g_dist -f n101c2naclprod2-12nsvrpr.trr -s
n101c2naclpose2prod2nsvrpr.tpr -n index.ndx -dist 0.35 -o
N101Cbest2NACL606S336HG1.xvg
and the output was distance calculated for every 10 frames in nm as under:
t: 11870 336 SER
On 2/11/13 6:15 PM, ram bio wrote:
Dear Gromacs Users,
I have a run a MD simulation on protein bound with ligand and ions
using Gromacs 4.5.4. I am able to calculate the distances between ions
and coordinating residues using g_dist. The output is in the form of
xvg file, but I am looking for t
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
Additionally to the new non-bonded SIMD kernels:
- Bonded force calculation got some SIMD acceleration which should
considerably improve performance;
- There have been be major improvements in PME (courtesy of Berk Hess &
Roland Schulz), you should see anywhere between up to 1.5-2x performance
impr
Dear Gromacs Users,
I have a run a MD simulation on protein bound with ligand and ions
using Gromacs 4.5.4. I am able to calculate the distances between ions
and coordinating residues using g_dist. The output is in the form of
xvg file, but I am looking for the occupancy for a cut off distance
(3.
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 Erik,
Many thanks for your comment.
The situation seems to be similar to TIP4P water model where the M
site is located among the three other atoms. In my case, it's between
the two C-H atoms.
Could I ask you which parameters must be selected for these virtual sites?
The interest molecule i
Try virtual sites constructions.
On Feb 11, 2013, at 6:01 PM, Rasoul Nasiri wrote:
Dear All,
I need to define interaction sites on the center of C-H bonds instead
of nuclei of each atom. The main reason was that non-bonding
parameters (sigma and epsilon) have been parametrized in these centers
Dear All,
I need to define interaction sites on the center of C-H bonds instead
of nuclei of each atom. The main reason was that non-bonding
parameters (sigma and epsilon) have been parametrized in these centers
and those are only available for the center of C-H.
So, I just wanted to know how ca
Last question (I hope).
How can I choose the force constant?
Indeed for the version 4.5, the force constant is defined by the
option dihre_fc in the mdp input file. After this force is multiply by
kfac contained in the dihedral_sections in the topology file
Now this option is obsolete. The f
Indeed - that's about the order of improvement expected for just switching
to 4.6 and proceeding as before on CPU-only hardware. Better use of SIMD
instructions and calling force-only kernels when energies are not required
are likely to be the code improvements leading to the performance
improvemen
Thanks for all your answers. I tried collecting data more frequently (100
fs), used -trestart as the entire trajectory; however my diffusion
coefficient for D2O is still in the range 1.4 - 1.5 e-5 cm^2/s.
Surprisingly, the number of Hbonds, potential energy, density are all what
would be expected f
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