[gmx-users] installing Gromacs4.6.3 with CPMD

2013-10-01 Thread Collins Nganou
Hallo everyone I would like to know if anyone has installed gromacs4.6.3 with CPMD, or how to monitor this installation? I couldn't find the installation procedure in the manual of gromacs4.6 I am looking forwards any suggestions. Thanks Collins -- gmx-users mailing listgmx-users@gromacs.o

Re: [gmx-users] ionomer topolgy

2013-10-01 Thread Justin Lemkul
On 10/1/13 1:03 PM, Ehsan Sadeghi wrote: Hello, When I use pdb2gmx, the bonds between atoms in the generated conf.gro or conf. pdb file are misplaced. I am using Avogadro for building the atomistic structure, it uses "connect" command to connect atom correctly. After running pdb2gmx, the gen

Re: [gmx-users] Re: g_hydorder

2013-10-01 Thread David van der Spoel
On 2013-10-01 19:51, Nidhi Katyal wrote: Please provide me with necessary guidance. I have already posted this thrice but have not got a single reply Thanks in advance. On Tue, Oct 1, 2013 at 3:40 PM, Nidhi Katyal wrote: Hello everyone, I would like to calculate angle tetrahedral order param

[gmx-users] Re: g_hydorder

2013-10-01 Thread Nidhi Katyal
Please provide me with necessary guidance. I have already posted this thrice but have not got a single reply Thanks in advance. On Tue, Oct 1, 2013 at 3:40 PM, Nidhi Katyal wrote: > Hello everyone, > > I would like to calculate angle tetrahedral order parameter of water > molecules as defined by

Re: [gmx-users] ionomer topolgy

2013-10-01 Thread Ehsan Sadeghi
Hello, When I use pdb2gmx, the bonds between atoms in the generated conf.gro or conf. pdb file are misplaced. I am using Avogadro for building the atomistic structure, it uses "connect" command to connect atom correctly. After running pdb2gmx, the generated files do not have "connect" and they

Re: [gmx-users] Installing Extended Genbox

2013-10-01 Thread Mark Abraham
Since that patch is already merged, Tegar can just check out the (default) master branch - see http://www.gromacs.org/Developer_Zone/Git. The CMake build works the same way. I would suggest just using /bin/genbox once you have built it, i.e. do not go to the trouble of installing the development ve

Re: [gmx-users] Installing Extended Genbox

2013-10-01 Thread Justin Lemkul
On 10/1/13 10:58 AM, Tegar Nurwahyu Wijaya wrote: Hi Mark, Thank you for your reply. Actually I am not trying to add it to the repository. I have gromacs 4.6 installed in my computer. When I was trying using genbox, an error occurred caused by memory lacking. After searched this mailing list,

Re: [gmx-users] Installing Extended Genbox

2013-10-01 Thread Tegar Nurwahyu Wijaya
Hi Mark, Thank you for your reply. Actually I am not trying to add it to the repository. I have gromacs 4.6 installed in my computer. When I was trying using genbox, an error occurred caused by memory lacking. After searched this mailing list, I got that extended genbox code that can fix my probl

[gmx-users] g_hydorder

2013-10-01 Thread Nidhi Katyal
Hello everyone, I would like to calculate angle tetrahedral order parameter of water molecules as defined by Chau et al (eq 3). I am using g_hydorder of gromacs 4.6.3 with my index group containing all oxygen atoms of water: g_hydorder -f *.xtc -s *.tpr -o file1.xpm file2.xpm -or file_1.out file_

Re: [gmx-users] OPLS/AA + TIP5P, anybody?

2013-10-01 Thread gigo
Dear Chris, By now 7ns of the MD passed without a single warning. Best Regards, Grzegorz P.s. The mdp: constraints = none integrator = md dt = 0.001; ps nsteps = 1000 ; total 10 ns nstcomm = 1000 nstxout =

Re: [gmx-users] Installing Extended Genbox

2013-10-01 Thread Mark Abraham
I would generally not try to add it to an existing source repository. Instead, follow one of the suggestions in http://www.gromacs.org/Developer_Zone/Git/Gerrit#How_do_I_get_a_copy_of_my_commit_for_which_someone_else_has_uploaded_a_patch.3f to check out that version. Mark On Tue, Oct 1, 2013 at