Dear users,
I am using Gromacs 4.5.4. I rerun the simulation using the following
command:
mdrun -s protein-RUN.tpr -cpi protein-RUN.cpt -append
Unfortunately remaining output didnt append to existing files
(protein-RUN.xtc, protein-RUN.edr,
protein-RUN.log). On the contrary remaining output
On Fri, 2012-02-24 at 11:03 -0700, Denny Frost wrote:
Thank you both for your replies. I currently have another ionic
liquid running just fine on the same gromacs build (compiled the tpr
file yesterday), so I am reluctant to conclude that the problem is
with the linking. Please let me know
On 25/02/2012 9:07 PM, ahmet yıldırım wrote:
Dear users,
I am using Gromacs 4.5.4. I rerun the simulation using the following
command:
mdrun -s protein-RUN.tpr -cpi protein-RUN.cpt -append
Unfortunately remaining output didnt append to existing files
(protein-RUN.xtc, protein-RUN.edr,
On 25/02/2012 6:45 PM, priya thiyagarajan wrote:
hello sir,
Thanks for your kind reply..
one small doubt sir.. its enough to give*mdrun -s md.tpr -cpi state.cpt
*
so that it ll automatically append my new data to the respective file ..
Only if you are happy with the default filenames.
Mark
On 25/02/2012 6:30 PM, venkatesh s wrote:
Hi
i got that error in the step of pdb2gmx what can i do
i read also
http://www.gromacs.org/Documentation/Errors#Residue_%27XXX%27_not_found_in_residue_topology_database
can any one tell exact reason and how i handle further
The exact reason is
Juliette N. wrote:
On 24 February 2012 16:52, Justin A. Lemkul jalem...@vt.edu
mailto:jalem...@vt.edu wrote:
Juliette N. wrote:
On 23 February 2012 21:18, Mark Abraham mark.abra...@anu.edu.au
mailto:mark.abra...@anu.edu.au
mailto:mark.abra...@anu.edu.__au
Hi GROMACS friends,
I am trying to put to peptide close to each other..
with the help of -editconf -ci and -nmol option ,the peptide can be put
randomly at different location, but they are far apart.
To solve problem I proceed as follow...
1. I make gro file , with
rama david wrote:
Hi GROMACS friends,
I am trying to put to peptide close to each other..
with the help of -editconf -ci and -nmol option ,the peptide can be put
randomly at different location, but they are far apart.
To solve problem I proceed as follow...
1.
Hi GROMACS friend,
Thank you Justin For guidance.
As I also doing your KALP-15 in DPPC tutorial,
In that you maintain remove initial periodicity of
DPPC..
What is means initial periodicity??
That is the reason I thought the peptides have
Initial periodicity.(As
rama david wrote:
Hi GROMACS friend,
Thank you Justin For guidance.
As I also doing your KALP-15 in DPPC tutorial,
In that you maintain remove initial periodicity of
DPPC..
What is means initial periodicity??
The molecules of DPPC were post-processed in such a
Today I've tried to model internal water and forced with some problems :)
I've built my system by transferring water from X-ray structure to my
model. Than I've minimized this new structure in vacuum and water still
present on the desired positions
1) But when I've made my complete system ( with
James Starlight wrote:
Today I've tried to model internal water and forced with some problems :)
I've built my system by transferring water from X-ray structure to my
model. Than I've minimized this new structure in vacuum and water still
present on the desired positions
1) But when I've
Hi,
I am using a cluster where user/local/bin has some old mpi executable. But, I
have installed openmpi-1.3 in my own home directory so that I can use that for
installing gromacs4.5.4 parallel version. I have also updated the path with the
openmpi bin directory and library directory in the
Sanku M wrote:
Hi,
I am using a cluster where user/local/bin has some old mpi executable.
But, I have installed openmpi-1.3 in my own home directory so that I can
use that for installing gromacs4.5.4 parallel version. I have also
updated the path with the openmpi bin directory and library
Sanku M wrote:
Hi,
I intially tried the following command line for config log:
./configure --prefix=/home/berne/jm3745/UTIL/GROMACS_4.5.4_MPI/
--program-suffix=_4mpi --disable-shared -enable-mpi
and in the bash_profile I had set the path for my desired mpi executable:
Thanking you Mark Abraham for your valuable suggestion
Here i used DNA Ligand Complex only is that any specific options is there?
Thanks
--
*S.VENKATESH,*
II M.Sc Bioinformatics,
Alagappa University,
Karaikudi-630003
Tamil Nadu,
India
svenkateshbioinformat...@gmail.com
--
gmx-users mailing
Hi Gomacians,
I want to use implicit wall.
I set the mdp parameters as follows.
nwall= 2
wall_type= 9-3
wall_r_linpot= 1
wall_atomtype= Au Au
wall_density = 58.01 58.01
wall_ewald_zfac = 3
Also set LJ
On 26/02/2012 3:13 PM, venkatesh s wrote:
Thanking you Mark Abraham for your valuable suggestion
Here i used DNA Ligand Complex only is that any specific options is there?
Please consider the advice here http://www.gromacs.org/Support about the
kind of content that requests for help should
Dear Gromacs Specialists,
My total time for simulation is 60 ps (600 ns) because I work with MARTINI
coarse-grained force field and this time is enough for my system, but when I do
g_analyze -ee, I take this warning:
Warning: tau2 is longer than the length of the data (864000)
the
On 26/02/2012 3:58 PM, dina dusti wrote:
Dear Gromacs Specialists,
My total time for simulation is 60 ps (600 ns) because I work with
MARTINI coarse-grained force field and this time is enough for my system,
Different observables converge over different time scales. The
autocorrelation
Dear Mark,
Thank you very much from your response.
Can you tell me what is the best solution for this warning, Please?
Warning: tau2 is longer than the length of the data (864000)
the statistics might be bad
In addition to this warning is related to error estimate for radius of gyration
and
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