I am doing simulation of metal clusters with membranes by position restrain
(with f=1000) the membrane. In this simulation the structure of metal
cluster is collapsed after entering into membrane. I want to preserves its
structure with out doing position restrain the metal cluster because it has
Hi Vitaly,
Impossible just for v4.6.3? It was certainly possible to create static
executables for a Cray XE using v4.6.1 (I know, because I have done
it). I followed the same procedure for 4.6.3 and have only managed to
get dynamic executables (which do not work) hence my question.
I
Thanks a lot.
On Tue, Jul 23, 2013 at 9:37 PM, Justin Lemkul jalem...@vt.edu wrote:
On 7/23/13 11:58 AM, bipin singh wrote:
Hello All,
I there any way to get a .tpr for C-alpha atoms from an all atom .tpr
file.
tpbconv -h, particularly point 3.
-Justin
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Dear All,
I am trying to use g_dos to calculate the DoS of a bio-water system.
However, I could not choose a certain group (e.g. the protein) from the index
file.
My command is like this :
g_dos -f x.trr -s x.tpr -n x.ndx
And, I also have tried to calculate the DoS of the protein individually
Please find below the gmxcheck output. Opposite to what I said earlier it does
contain warning messages.
Thanks a lot for any suggestion.
gmxcheck output:
Option Filename Type Description
-f
Dear Carsten,
Thank you very much for your very useful help!
I'm making some tries to test the orire options that probably will solve my
problem.
In order to do not waste resource, I thought using the rerun option of mdrun I
can use the trajectories generated before, where my mistake was to
On 2013-07-24 01:57, Jonathan Saboury wrote:
I just finished this tutorial and found it very informative:
http://cinjweb.umdnj.edu/~kerrigje/pdf_files/trp_drug_tutor.pdf
However, This was based on a complex from a pdb.
I was wondering if it was possible to just simulate the protein without
On Jul 24, 2013, at 12:30 PM, battis...@libero.it wrote:
Dear Carsten,
Thank you very much for your very useful help!
I'm making some tries to test the orire options that probably will solve my
problem.
In order to do not waste resource, I thought using the rerun option of mdrun
I
On 7/24/13 6:44 AM, David van der Spoel wrote:
On 2013-07-24 01:57, Jonathan Saboury wrote:
I just finished this tutorial and found it very informative:
http://cinjweb.umdnj.edu/~kerrigje/pdf_files/trp_drug_tutor.pdf
However, This was based on a complex from a pdb.
I was wondering if it was
On 7/24/13 5:49 AM, Davit Hakobyan wrote:
Please find below the gmxcheck output. Opposite to what I said earlier it does
contain warning messages.
Thanks a lot for any suggestion.
gmxcheck output:
Option Filename Type Description
On 7/24/13 2:55 AM, Sathish Kumar wrote:
I am doing simulation of metal clusters with membranes by position restrain
(with f=1000) the membrane. In this simulation the structure of metal
cluster is collapsed after entering into membrane. I want to preserves its
structure with out doing
Dear All,
I want to calculate interaction energy per residue.
Below is the command i used:
g_enemat -f strand.edr -groups groups.dat -emat strand_emat.xpm
my groups.dat file contains these lines:
3
strand1_SER_34
strand1_THR_36
strand1_TYR_37
When i execute the above g_enemat command i get
in my traj.xtc file there are 1 frame every 10 ps from 0 ps to 1 ps,
therefore in total 1001 frames.
I tried -x trj.xtc instead -o trj.trr, but mdrun has generated a file trj.xtc.
trr
Many thanks!
Anna
Messaggio originale
Da: ckut...@gwdg.de
Data: 24/07/2013 13.09
A:
On 24.07.2013 04:08, Carlos Bueno wrote:
*Hi,*
*I keep getting errors when I try to install gromacs in OpenSuse 12.1.*
*I have installed cuda 5.0 and the nvidia cards. **I have tried with
different parameters for cmake:*
How did you install Cuda5? What did you install and how?
I have one
Dear Users,
I would like to know if anyone may help me understand how to update the
index file.
I am trying to simulate a dna in solution.
I have relaxed a Solvent with attached min.mdp file without problem. in
the second step I was intended to relax SOL + Na DNA with 20ps.mdp. But
the index
On 7/24/13 8:34 AM, Collins Nganou wrote:
Dear Users,
I would like to know if anyone may help me understand how to update the
index file.
I am trying to simulate a dna in solution.
I have relaxed a Solvent with attached min.mdp file without problem. in
the second step I was intended to relax
On 7/24/13 7:47 AM, Poojari, Chetan wrote:
Dear All,
I want to calculate interaction energy per residue.
Below is the command i used:
g_enemat -f strand.edr -groups groups.dat -emat strand_emat.xpm
my groups.dat file contains these lines:
3
strand1_SER_34
strand1_THR_36
strand1_TYR_37
Thank you again for your time and help.
Performing rerun on the original system passes without warnings with the
following output:
Option Filename Type
On 7/24/13 9:25 AM, Davit Hakobyan wrote:
Thank you again for your time and help.
Performing rerun on the original system passes without warnings with the
following output:
Hi,
I am trying to run US on a system composed of lipid bilayer/ ion/ water/
peptide. The peptide is inserted through the lipid bilayer and I' d like to
study the ion conduction through the peptide across the membrane.
In order to do so, I tried to set a specific ion ( Ces with the atom number
On 7/24/13 11:30 AM, Shima Arasteh wrote:
Hi,
I am trying to run US on a system composed of lipid bilayer/ ion/ water/
peptide. The peptide is inserted through the lipid bilayer and I' d like to
study the ion conduction through the peptide across the membrane.
In order to do so, I tried to
Dear Carsten
could you give me more information about your suggestions?
I tried but probably I did not understand well what you meant.
In order to avoid the rotation of the structure A and of the structure B, I
have defined into the index file a group A_B that contains A+B and I have
setted
Yes, Thanks.
Would you give me a hint on this fact that how I would be sure that I am
running a correct US ? with proper settings?
To save time, I' d prefer to run the US.mdp just for one window. Do you agree
with me that if I run an incorrect US for any of the windows, I would get an
odd
I am fairly new to gromacs and I am trying to run a thermodynamic
integration simulation of a ligand disappearing in a box of octanol at a
single set lambda point. I have previous successful nvt and npt runs of
this system. When I have added the free energy portions to the input file,
I get the
On 7/24/13 4:33 PM, Scott Pendley wrote:
I am fairly new to gromacs and I am trying to run a thermodynamic
integration simulation of a ligand disappearing in a box of octanol at a
single set lambda point. I have previous successful nvt and npt runs of
this system. When I have added the free
For the rest of us mere mortals who don't have access to specialized hardware
that allows for 10- or 20-microsecond simulations, the brute force approach is
rather futile. Techniques like steered MD and Hamiltonian replica exchange MD
are probably more feasible. Unbiased simulations of
On 7/24/13 9:16 PM, Jonathan Saboury wrote:
For the rest of us mere mortals who don't have access to specialized hardware
that allows for 10- or 20-microsecond simulations, the brute force approach is
rather futile. Techniques like steered MD and Hamiltonian replica exchange MD
are probably
In an implicit, non-periodic system, it is more likely that the ligand
will
float away from the protein. I've tried it and that's all that ever
happens.
Moreover, the current Gromacs version does not support implicit solvent on
GPU
and the previous version that did had very limited functionality.
Hello:
I notice that the manual or tutorial in Gromacs (FEP, unbralla
sampling, TI and so on) website for binding energy evaluation are all
for protein in water. I am just wondering how can we evaluate the
protein/ligand binding affinity for membrane system accurately? Probably
the most
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