[gmx-users] get a representative frame

2013-11-29 Thread aixintiankong
Dear, i want to get a representative frame from a trajectory to analyze the interaction between the protein and ligand. first i use the g_rms command to get the rmsd-matrix.xpm file from 80ns to 100ns. The min rmsd is 0 and the max is 6. The next step i will use the g_culster to get the rep

[gmx-users] get a representative frame

2013-11-29 Thread aixintiankong
Dear, i want to get a representative frame from a trajectory to analyze the interaction between the protein and ligand. first i use the g_rms command to get the rmsd-matrix.xpm file from 80ns to 100ns. The min rmsd is 0 and the max is 6. The next step i will use the g_culster to get the rep

[gmx-users] GMX_THREAD_MPI=ON" does not exis

2013-11-29 Thread Mahboobeh Eslami
hi my friends, please help me i use following command for install gromacs: CMAKE_PREFIX_PATH=/usr/local/openmpi/:/home/elahe/ComTools/fftw/ cmake .. -DGMX_MPI=ON GMX_THREAD_MPI=ON -DBUILD_SHARED_LIBS=OFF -DGMX_PREFER_STATIC_LIBS=ON -DGMX_DOUBLE=ON -DCMAKE_INSTALL_PREFIX=/home/elahe/ComTools/gr

Re: [gmx-users] GMX_THREAD_MPI=ON" does not exis

2013-11-29 Thread Hardy, Adam
You seem to be missing a -D infront of the thread mpi option. On 29 Nov 2013 16:54, Mahboobeh Eslami wrote: hi my friends, please help me i use following command for install gromacs: CMAKE_PREFIX_PATH=/usr/local/openmpi/:/home/elahe/ComTools/fftw/ cmake .. -DGMX_MPI=ON GMX_THREAD_MPI=ON -DBUIL

Re: [gmx-users] GMX_THREAD_MPI=ON" does not exis

2013-11-29 Thread Mahboobeh Eslami
Thank you for your help What command do I use to use 8 cores Good luck On Friday, November 29, 2013 7:22 PM, Mahboobeh Eslami wrote: hi my friends, please help me i use following command for install gromacs: CMAKE_PREFIX_PATH=/usr/local/openmpi/:/home/elahe/ComTools/fftw/ cmake .. -DGMX

[gmx-users] valid command line argument do i use by mdrun_mpi_d for 8 cores.

2013-11-29 Thread Mahboobeh Eslami
i want to install gromacs4.6.3 on 8 core. i use following command: CMAKE_PREFIX_PATH=/usr/local/openmpi/:/home/elahe/ComTools/fftw/ cmake .. -DGMX_MPI=ON -DGMX_THREAD_MPI=ON -DBUILD_SHARED_LIBS=OFF -DGMX_PREFER_STATIC_LIBS=ON -DGMX_DOUBLE=ON -DCMAKE_INSTALL_PREFIX=/home/elahe/ComTools/gromacs i

Re: [gmx-users] valid command line argument do i use by mdrun_mpi_d for 8 cores.

2013-11-29 Thread Hardy, Adam
As far as I understand, if you have configured it correctly with that version, it will use all available cores unless you specify otherwise. The precise command for this escapes me for the moment but it is documented on the gromacs website. When you run mdrun it will tell you how many threads it

Re: [gmx-users] valid command line argument do i use by mdrun_mpi_d for 8 cores.

2013-11-29 Thread Mark Abraham
You don't; you configure your MPI environment to have 8 ranks, which could be as simple as mpirun -np 8 mdrun_mpi. Generally you do not need double precision with GROMACS, unless you can say exactly why you need to trade away your simulation performance. Mark On Nov 29, 2013 9:15 PM, "Mahboobeh E

[gmx-users] pdb2gmx fails because of imaginary "Residue E"

2013-11-29 Thread kolnkempff
pdb2gmx produces error message: Fatal error: Residue 'E' not found in residue topology database But there is no "Residue 'E' " in my pdb file (see below). I have verified that all residues in the pdb file are listed in ffamber03.rtp and pdb2gmx does identify the ACE and NME caps. COMPNDUNNA

Re: [gmx-users] pdb2gmx fails because of imaginary "Residue E"

2013-11-29 Thread Justin Lemkul
On 11/29/13 7:23 PM, kolnkempff wrote: pdb2gmx produces error message: Fatal error: Residue 'E' not found in residue topology database But there is no "Residue 'E' " in my pdb file (see below). I have verified that all residues in the pdb file are listed in ffamber03.rtp and pdb2gmx does iden

Re: [gmx-users] Regarding soft core parameter: Relative solvation free energy calculation

2013-11-29 Thread Michael Shirts
The fluctuation is often of the order of magnitude of itself. It's that matters. On Thu, Nov 28, 2013 at 1:26 PM, bipin singh wrote: > Thanks for you reply Prof. Shirts. > > I have plotted the dh/dl values (link mentioned below), but I am not sure > whether the fluctuation is in acceptable ra

Re: [gmx-users] Regarding soft core parameter: Relative solvation free energy calculation

2013-11-29 Thread bipin singh
Thank you Prof. Shirts for your help and suggestions. On Sat, Nov 30, 2013 at 6:04 AM, Michael Shirts wrote: > The fluctuation is often of the order of magnitude of itself. > It's that matters. > > > > On Thu, Nov 28, 2013 at 1:26 PM, bipin singh wrote: > > Thanks for you reply Prof. Shirts.

[gmx-users] retrieve box size from .trr or .tpr

2013-11-29 Thread Saman Shahriyari
Dear users is there any way to retrieve box size and othe properties from .trr or .tpr file? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists