Re: [gmx-users] CMake Error at cmake/gmxManageSimd.cmake:67 (message): Found a compiler flag for AVX2 support, but some other problem exists.

2016-09-04 Thread Justin Lemkul
On 9/4/16 2:52 PM, Atila Petrosian wrote: Dear Justin, Thanks for your good guidance (There is only one program now.). My previous problem was solved. Now, I have another question. I used two times following commands for my system (protein): gmx_mpi mdrun -v -deffnm npt >& npt_1.job & gm

[gmx-users] CMake Error at cmake/gmxManageSimd.cmake:67 (message): Found a compiler flag for AVX2 support, but some other problem exists.

2016-09-04 Thread Atila Petrosian
Dear Justin, Thanks for your good guidance (There is only one program now.). My previous problem was solved. Now, I have another question. I used two times following commands for my system (protein): gmx_mpi mdrun -v -deffnm npt >& npt_1.job & gmx_mpi mdrun -nb gpu -v -deffnm npt >& npt_2.j

Re: [gmx-users] CMake Error at cmake/gmxManageSimd.cmake:67 (message): Found a compiler flag for AVX2 support, but some other problem exists.

2016-09-04 Thread Justin Lemkul
On 9/4/16 1:45 PM, Atila Petrosian wrote: Dear Mark, In /usr/local/gromasc/bin directory, there are only demux.pl gmx-completion.bash gmx-completion-gmx_mpi.bash gmx_mpi GMXRC GMXRC.bash GMXRC.csh GMXRC.zshxplor2gmx.pl In this directory, there is gmx_mpi rather than gmx. It is true based on

[gmx-users] CMake Error at cmake/gmxManageSimd.cmake:67 (message): Found a compiler flag for AVX2 support, but some other problem exists.

2016-09-04 Thread Atila Petrosian
Dear Mark, In /usr/local/gromasc/bin directory, there are only demux.pl gmx-completion.bash gmx-completion-gmx_mpi.bash gmx_mpi GMXRC GMXRC.bash GMXRC.csh GMXRC.zshxplor2gmx.pl In this directory, there is gmx_mpi rather than gmx. It is true based on the http://manual.gromacs.org/documentation/5

[gmx-users] CMake Error at cmake/gmxManageSimd.cmake:67 (message): Found a compiler flag for AVX2 support, but some other problem exists.

2016-09-04 Thread Atila Petrosian
Dear Mark, > you still need to source the GMXRC from the version you want to use > > in > the terminal you want to use it from. I used source /usr/local/gromacs/bin/GMXRC, But, when I use gmx pdb2gmx command, I encountered with: -bash: gmx: command not found Best, Atila -- Gromacs Users mail

Re: [gmx-users] CMake Error at cmake/gmxManageSimd.cmake:67 (message): Found a compiler flag for AVX2 support, but some other problem exists.

2016-09-04 Thread Mark Abraham
Hi, Like the installation instructions say, you still need to source the GMXRC from the version you want to use in the terminal you want to use it from. Mark On Sun, 4 Sep 2016 16:02 Atila Petrosian wrote: > Dear Justin, > > Thanks for your answer. > > I know several programs have been renamed

[gmx-users] CMake Error at cmake/gmxManageSimd.cmake:67 (message): Found a compiler flag for AVX2 support, but some other problem exists.

2016-09-04 Thread Atila Petrosian
Dear Justin, Thanks for your answer. I know several programs have been renamed in new version such as pdb2gmx --> gmx pdb2gmx. But when I use gmx pdb2gmx, -bash: gmx: command not found Best, -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_L

Re: [gmx-users] CMake Error at cmake/gmxManageSimd.cmake:67 (message): Found a compiler flag for AVX2 support, but some other problem exists.

2016-09-04 Thread Justin Lemkul
On Sunday, September 4, 2016, Atila Petrosian wrote: > Dear Mark, > > Thanks for your quick answer. > > Now, how to use gromacs 5.1.3 commands? > > The reason of my question: > > There is gromacs 4.5.4 (in /opt/bio directory) in my Rocks cluster system > by default. > > I used source /usr/local/g

[gmx-users] CMake Error at cmake/gmxManageSimd.cmake:67 (message): Found a compiler flag for AVX2 support, but some other problem exists.

2016-09-04 Thread Atila Petrosian
Dear Mark, Thanks for your quick answer. Now, how to use gromacs 5.1.3 commands? The reason of my question: There is gromacs 4.5.4 (in /opt/bio directory) in my Rocks cluster system by default. I used source /usr/local/gromacs/bin/GMXRC, then pdb2gmx Unfortunately, pdb2gmx related to gromac

Re: [gmx-users] CMake Error at cmake/gmxManageSimd.cmake:67 (message): Found a compiler flag for AVX2 support, but some other problem exists.

2016-09-04 Thread Mark Abraham
Hi, Yes. http://manual.gromacs.org/documentation/5.1/ReleaseNotes/removed-features.html#removed-temporary-symlinks-from-pre-5-0-tool-names Mark On Sun, Sep 4, 2016 at 3:19 PM Atila Petrosian wrote: > Dear Mark, > > Thanks for the guidance. > > I updated gcc using your proposed link (https://ed

[gmx-users] CMake Error at cmake/gmxManageSimd.cmake:67 (message): Found a compiler flag for AVX2 support, but some other problem exists.

2016-09-04 Thread Atila Petrosian
Dear Mark, Thanks for the guidance. I updated gcc using your proposed link (https://ed.braaten.net/blog/ 2014-05-28-devtools-for-centos/). Now my Rocks cluster system has following info: Rocks 6.2 CentOS 6.6 Cuda 7.5 and 8 (/usr/local/cuda) gcc 4.8.2 I installed gromacs 5.1.3 based on followin

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 149, Issue 12

2016-09-04 Thread prithvi raj pandey
Dear James, Thank you for your reply. I have tried the trjconv for fixing PBC and it works fine. I posted this query because I came across the following very old thread https://redmine.gromacs.org/issues/165 thus I wanted to make sure everything is fine. Thanking you, Prithvi > - > > Messag

[gmx-users] Including TIP3P water molecules in GB model.

2016-09-04 Thread Dd H
Hi, I think some crystal water molecules are important to my the system. Can I keep the crystal water molecules when I run a MD simulation with implicit water model? Thank you in advance! Best regards! Dading Huang -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.