Re: [gmx-users] Simulation of membrane protein

2011-10-16 Thread Justin A. Lemkul
James Starlight wrote: Justin, hello! In the algorthm presented in the tutorial there is one inconvenience that is many iterations of the shrinking/minimization of the protein ( e.g if i'd like to obrain good value for S per lipid for my structure). Is there any way to make this process aut

Re: [gmx-users] Link to Intel MKL (fftw) via cmake options

2011-10-16 Thread Mark Abraham
On 15/10/2011 9:02 PM, Mirco Wahab wrote: On 10/15/2011 1:15 AM, Mark Abraham wrote: I use ccmake ..\ -DGMX_FFT_LIBRARY=mkl "\ -DMKL_LIBRARIES=${MKL}/lib/em64t/libmkl_intel_thread.so;${MKL}/lib/em64t/libmkl_lapack.so;${MKL}/lib/em64t/libmkl_core.so;${MKL}/lib/em64t/libmkl_em64t.a;${MKL}/lib/em6

[gmx-users] about the pulling

2011-10-16 Thread Tom
Dear Gromacs Users or Developers, I am using the pulling the COM of object A towards B using: - pull = umbrella pull_geometry= distance pull_dim = N N Y pull_start = yes pull_ngroups = 1 pull_

Re: [gmx-users] about the pulling

2011-10-16 Thread Justin A. Lemkul
Tom wrote: Dear Gromacs Users or Developers, I am using the pulling the COM of object A towards B using: - pull = umbrella pull_geometry= distance pull_dim = N N Y pull_start = yes pull_ngroups

[gmx-users] Fwd: about the pulling

2011-10-16 Thread Tom
Justin you have good experience of pulling. If you have time, please help with this publling problem: abrupt change in sign of 1dZ on output file: pullx.xvg. Thanks a lot! i am pulling A object towards B along z-axis. But system has pbc on x, y and z. Is it because of the pbc image of B object t

[gmx-users] Re: Fwd: about the pulling

2011-10-16 Thread Justin A. Lemkul
Tom wrote: Justin you have good experience of pulling. If you have time, please help with this publling problem: abrupt change in sign of 1dZ on output file: pullx.xvg. Thanks a lot! I already commented: http://lists.gromacs.org/pipermail/gmx-users/2011-October/065226.html i am pulling

Re: [gmx-users] Link to Intel MKL (fftw) via cmake options

2011-10-16 Thread Mirco Wahab
On 10/16/2011 2:25 PM, Mark Abraham wrote: On 15/10/2011 9:02 PM, Mirco Wahab wrote: On 10/15/2011 1:15 AM, Mark Abraham wrote: I use ... ... //Flags used by the compiler during all build types CMAKE_CXX_FLAGS:STRING=' -msse2 -ip -funroll-all-loops -std=gnu99 ' //Flags used by the compiler du

[gmx-users] oops, s/gcc 4.5.1/icc 12.1.0/

2011-10-16 Thread Mirco Wahab
On 10/16/2011 10:04 PM, Mirco Wahab wrote: - gcc 4.5.1 x64 (Linux) (20101208) with the said gcc, all builds works fine, the problem arises with the Intel suite (icc/icpc 12.1.0) sorry for the typo. M. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo

[gmx-users] g_hbond frames

2011-10-16 Thread Yao Yao
Hi Gmxers, I ran g_hbond between my protein and water for a 3ns trajectory with 2 fs integration step but found the error, "Cannot calculate autocorrelation of life times with less than two frames", I am quite sure my system is just a regular protein in a cubic water box. And the size of traj

Re: [gmx-users] g_hbond frames

2011-10-16 Thread Justin A. Lemkul
Yao Yao wrote: Hi Gmxers, I ran g_hbond between my protein and water for a 3ns trajectory with 2 fs integration step but found the error, "Cannot calculate autocorrelation of life times with less than two frames", I am quite sure my system is just a regular protein in a cubic water box. An

[gmx-users] topologies for POPE and DMPE

2011-10-16 Thread Roy Lee
Dear all, I would like to simulate my protein in a lipid bilayer using gromacs 4.5.4, and a forcefield of gromos96. However i don't have the topologies files for lipid bilayer for POPE and DMPE. Anybody knows where can i get the topologies file for POPE and DMPE ? Any help is much appreciated

Re: [gmx-users] Link to Intel MKL (fftw) via cmake options

2011-10-16 Thread Mark Abraham
On 17/10/2011 7:04 AM, Mirco Wahab wrote: On 10/16/2011 2:25 PM, Mark Abraham wrote: On 15/10/2011 9:02 PM, Mirco Wahab wrote: On 10/15/2011 1:15 AM, Mark Abraham wrote: I use ... ... //Flags used by the compiler during all build types CMAKE_CXX_FLAGS:STRING=' -msse2 -ip -funroll-all-loops -s

[gmx-users] trjconv:solute at the center

2011-10-16 Thread Nilesh Dhumal
Hello, I have system with solute is surrounded by 256 solvent molecules. I run the simulation for 20 ns. I save the snap shot at 500 ps using following command. trjconv -f 3.trr -s 3.tpr -n 500-1.ndx -b 500.0 -e 501.0 -dt 1.0 -pbc nojump -center -o 500-11.pdb I tried to keep the solute at the

[gmx-users] cyclosporine A

2011-10-16 Thread Алексей Раевский
Hi! I need an advice concerninng topology building of such substance like cyclosporine A. I've tried to make it with antechamber tool, cause I wanted to use amber99sb forcefield. But the program gave me an error in the begining and no results in the end after 12 hours of calculations ))) Can you gi