In addition to my previous question, I have another question about
g_analyze. When I used the hbond.xvg file to get the average and plotted
the average.xvg file I found that the average value is round 4 to 5
according to the graph. But g_analyze in its final calculation gives 7.150
as the average
Hi
I am confusing with the output file (.log) about the sample frequency (frames)
in my simulation. The average information in .log file is 'Statistics over
31 steps using 3001 frames' where nstxout =4000 and nstlog =4000. While,
'Statistics over 31 steps using 20001 frames', appeared
On 11/11/13 1:30 AM, bharat gupta wrote:
thank you informing about g_rdf...
Is it possible to dump the structure with those average water molecules
interacting with the residues. I generated the hbond.log file which gives
the details but I need to generate a figure for this ??
g_select
On 11/11/13 4:06 AM, bharat gupta wrote:
In addition to my previous question, I have another question about
g_analyze. When I used the hbond.xvg file to get the average and plotted
the average.xvg file I found that the average value is round 4 to 5
according to the graph. But g_analyze in its
On 11/11/13 5:04 AM, guozhicheng222 wrote:
Hi
I am confusing with the output file (.log) about the sample frequency
(frames) in my simulation. The average information in .log file is
'Statistics over 31 steps using 3001 frames' where nstxout =4000 and
nstlog =4000. While, 'Statistics over
Dear gmx-users,
I am trying to install gromacs-4.6.3 on an older Dell that is running
openSuse 12.2
Using DGMX_BUILD_OWN_FFTW=ON failed for me so to get through cmake I had
to compile fftw from scratch and I followed the recommendation of going
directly to their website. Now I am at the make
On 11/11/13 11:24 AM, Carlos Javier Almeciga Diaz wrote:
Hello evryone,
I doing a simulation of a ligand-protein interaction with gromacs 4.5.5.
Everything looks fine after I equilibrate the protein-ligand complex. I'm
running these commands:
grompp -f nvt.mdp -c em.gro -p topol.top -n
Hello evryone,
I doing a simulation of a ligand-protein interaction with gromacs 4.5.5.
Everything looks fine after I equilibrate the protein-ligand complex. I'm
running these commands:
grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr
mdrun -deffnm nvt
Nevertheless, I got
On 11/11/13 11:27 AM, kolnkempff wrote:
Dear gmx-users,
I am trying to install gromacs-4.6.3 on an older Dell that is running
openSuse 12.2
Using DGMX_BUILD_OWN_FFTW=ON failed for me so to get through cmake I had
to compile fftw from scratch and I followed the recommendation of going
Hello
If I did the MD simulation using PME and neutralized with ions, and I want
to rerun this time with reaction field zero, is there any problem if I
keep the ions? This is for LIE calculation. I am using AMBER99SB.
Thanks
Williams
--
gmx-users mailing listgmx-users@gromacs.org
Dear gromacs users,
I have NaCl-water system of finite concentration .I want to calculate
water-water hydrogen bond in the first solvation shell around ion..So I
used g_hbond -shell option.For single ion in water,its easy to
calculate..But say,for water-water hydrogen bonds around two Na+ ions,it
11 matches
Mail list logo