[gmx-users] distance_restraints

Hi, all I use GMX4.5.5, GROMOS96 53a6 force field ro simulation 1dx0.pdb, I use two steps energy minimization (steep and cg ) in vacuum as follows: 1. pdb2gmx -f 1dx0.pdb -o xxx.gro -ignh -ter -water spce -ss -p xxx.top 2. editconf -f xxx.gro -o xxx.pdb -c -d 0.9 -bt cubic 3.grompp -f

Re: [gmx-users] distance_restraints

On 6/9/13 5:15 AM, maggin wrote: Hi, all I use GMX4.5.5, GROMOS96 53a6 force field ro simulation 1dx0.pdb, I use two steps energy minimization (steep and cg ) in vacuum as follows: 1. pdb2gmx -f 1dx0.pdb -o xxx.gro -ignh -ter -water spce -ss -p xxx.top 2. editconf -f xxx.gro -o xxx.pdb

Re: [gmx-users] Eigenvector and eigenvalues

Hi Tsjerk, Thank you so much for the helpful insight. It will surely help in clearing some basic concepts about eigenvectors and the projections. Also, since in the end you mentioned about my matrix being derived only from C-alpha atoms which proves a limitation, would you reckon a backbone

[gmx-users] g_density -center issues (GMX version 4.6)

Hi users/developers, I identified 2 issues in the center_coords function of g_density that make the flag -center incorrectly center the system. These are in addition to the issues previously raised by Chris Neale (reported as issue 1168 on redmine: http://redmine.gromacs.org/issues/1168). I have

Re: [gmx-users] GPU ECC question

On Sat, Jun 8, 2013 at 9:21 PM, Albert mailmd2...@gmail.com wrote: Hello: Recently I found a strange question about Gromacs-4.6.2 on GPU workstaion. In my GTX690 machine, when I run md production I found that the ECC is on. However, in my another GTX590 machine, I found the ECC was off: 4

Re: [gmx-users] Running gmx-4.6.x over multiple homogeneous nodes with GPU acceleration

On Wed, Jun 5, 2013 at 4:35 PM, João Henriques joao.henriques.32...@gmail.com wrote: Just to wrap up this thread, it does work when the mpirun is properly configured. I knew it had to be my fault :) Something like this works like a charm: mpirun -npernode 2 mdrun_mpi -ntomp 8 -gpu_id 01

[gmx-users] Re: mdrun segmentation fault for new build of gromacs 4.6.1

Roland, I have posted the cmake output (cmake-4.6.1) and the file CMakeError.log at the usual https://www.dropbox.com/sh/h6867f7ivl5pcl9/j9gt9CsVdP I see there are some errors but don't know what to make of them. Thanks, Amil -- View this message in context:

Re: [gmx-users] Re: mdrun segmentation fault for new build of gromacs 4.6.1

Hi, based on Mark's idea I would have thought that the cpu detection would have already failed during cmake. But it seems it detected SSE4.1 correctly. Could you post the stack trace for the crash? (see previous mail for instructions) Roland On Sun, Jun 9, 2013 at 4:42 PM, Amil Anderson

[gmx-users] fftw without SIMD

Dear gromacs users, I am compiling gromacs 4.6.1, but when I configure the package ccmake says: The fftw library found is compiled without SIMD support, which makes it although I compiled fftw ./configure --enable-single --enable-shared --enable-sse2 CC=icc F77=ifort CFLAGS=-msse4.1 Is it a

[gmx-users] ask for help

Dear, sir I'm a user of gromacs from China.I have just regist your mail list.gmx-users mailing list membership configuration for mxy1989 at mail.ustc.edu.cn, bravema. but I don't know how to use it. and I have a very important question: In your gromacs version 4.5 , Pulling is not

[gmx-users] building OLPSAA force field

Dear Gromacs users, I'm still relatively new to molecular modelling. I want to build a OPLSAA toplogy file of my molecule. I have only the pdb file of my molecule. Can any one help me what detailed steps should I follow to get that topolgy file. Many thanks -- gmx-users mailing list

Re: [gmx-users] fftw without SIMD

You may have compiled one like that (AFAIK those CFLAGS won't help), but CMake *finding* that one once installed can be another matter (e.g. use CMAKE_PREFIX_PATH per install instructions). You can see which fftw was found with grep FFTWF_LIBRARY CMakeCache.txt from the build directory - or pay

Re: [gmx-users] building OLPSAA force field

Hi, Please do search for GROMACS tutorial material, which will help you get started with the basic concepts. Cheers, Mark On Mon, Jun 10, 2013 at 6:34 AM, Souilem Safa safasouil...@gmail.comwrote: Dear Gromacs users, I'm still relatively new to molecular modelling. I want to build a

Re: [gmx-users] building OLPSAA force field

Dear Mark, thank you for your answer, I'm doing it right now. Cheers, Safa On 10 June 2013 14:02, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, Please do search for GROMACS tutorial material, which will help you get started with the basic concepts. Cheers, Mark On Mon, Jun 10,