Re: [gmx-users] Re: g_analyze

2013-11-11 Thread bharat gupta
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

[gmx-users] help about logfile

2013-11-11 Thread guozhicheng222
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

Re: [gmx-users] Re: g_analyze

2013-11-11 Thread Justin Lemkul
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

Re: [gmx-users] Re: g_analyze

2013-11-11 Thread Justin Lemkul
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

Re: [gmx-users] help about logfile

2013-11-11 Thread Justin Lemkul
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

[gmx-users] installation error under openSuse 12.2

2013-11-11 Thread kolnkempff
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

Re: [gmx-users] segmentation fault on gromacs 4.5.5 after mdrun

2013-11-11 Thread Justin Lemkul
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

[gmx-users] segmentation fault on gromacs 4.5.5 after mdrun

2013-11-11 Thread Carlos Javier Almeciga Diaz
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

Re: [gmx-users] installation error under openSuse 12.2

2013-11-11 Thread Justin Lemkul
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

[gmx-users] Re: Reaction field zero and ions

2013-11-11 Thread Williams Ernesto Miranda Delgado
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

[gmx-users] hydrogen bond calculation problem

2013-11-11 Thread Sushma Yadav
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