Re: [gmx-users] [gmx-developers] GTX 680 non detected on OS X

> So to summarize: > >- your installation does have shared libraries (we know); >- you set CUDA*USE*STATIC*CUDA*RUNTIME=OFF (which is what the change >does and what you can also do manually in cmake) ? >- and you are still getting gmx statically linked against libcudart? > > >

Re: [gmx-users] Error while generating ions.tpr file

The text of the error has nothing to do with the ions you may or may not need to add. Please read more closely. Mark On Wed, 1 Jun 2016 06:57 kamakshi sikka wrote: > Hello, > > I am doing mixed lipid bilayer simulation with a peptide. This bilayer > membranewas built

[gmx-users] Error while generating ions.tpr file

Hello, I am doing mixed lipid bilayer simulation with a peptide. This bilayer membranewas built by Charmm Gui. Afterwards, I oriented the peptide on the top of the bilayer and then saved the peptide+membrane complex file. Then , I am trying to add ions into the system by giving the command

Re: [gmx-users] Error while re-compiling Gromacs 5.1.2 with GPU and gcc 5.3.1

Either approach can work, but you could have tried your command before emailing :-) Mark On Wed, 1 Jun 2016 00:35 Diogo Martins de Sá wrote: > Hi Mark and Szilard, > > Thanks for all the help. Just to make sure I understood, I should run > cmake like this: > > cmake ..

Re: [gmx-users] Error while re-compiling Gromacs 5.1.2 with GPU and gcc 5.3.1

Hi Mark and Szilard, Thanks for all the help. Just to make sure I understood, I should run cmake like this: cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=on -DGPU_DEPLOYMENT_KIT_ROOT_DIR=/usr/local/cuda-7.5 -DCMAKE_C_FLAGS="-D_FORCE_INLINES" or should I try to modify a

Re: [gmx-users] Error while re-compiling Gromacs 5.1.2 with GPU and gcc 5.3.1

Hi, That's the standard content of CUDA - that deliberate compiler error has to be suppressed (per the link in the original post) if you want to use a different compiler. The issue here is that the version of the C standard library that ships on the operating system has a new feature that

Re: [gmx-users] Error while re-compiling Gromacs 5.1.2 with GPU and gcc 5.3.1

Em 31-05-2016 17:25, Szilárd Páll escreveu: Hi, Just because gcc 5.3 and CUDA/nvcc 7.5 are in some Ubuntu repos (partner AFAIR), it does not mean they're automatically compatible. The NVIDIA documentation clearly indicates they're not. Surely the ubuntu cuda maintainers patched

Re: [gmx-users] Error while re-compiling Gromacs 5.1.2 with GPU and gcc 5.3.1

On Tue, May 31, 2016 at 10:25 PM, Szilárd Páll wrote: > Hi, > > Just because gcc 5.3 and CUDA/nvcc 7.5 are in some Ubuntu repos (partner > AFAIR), it does not mean they're automatically compatible. The NVIDIA > documentation clearly indicates they're not. > > However, this

Re: [gmx-users] Error while re-compiling Gromacs 5.1.2 with GPU and gcc 5.3.1

On Tue, May 31, 2016 at 10:09 PM, Diogo Martins de Sá wrote: > Hi Florent, > > you''ve read my mind! I've just tried that using gcc-4.8 and g++-4.8. > > the "cmake" step worked like before but "make" gave the exact same error. > That's because the issue is in a system

Re: [gmx-users] Error while re-compiling Gromacs 5.1.2 with GPU and gcc 5.3.1

Hi, Just because gcc 5.3 and CUDA/nvcc 7.5 are in some Ubuntu repos (partner AFAIR), it does not mean they're automatically compatible. The NVIDIA documentation clearly indicates they're not. However, this typically means that minor issue can prevent building. In this case, it looks like a

Re: [gmx-users] Error while re-compiling Gromacs 5.1.2 with GPU and gcc 5.3.1

Hi Florent, you''ve read my mind! I've just tried that using gcc-4.8 and g++-4.8. the "cmake" step worked like before but "make" gave the exact same error. Does anyone know what the "Building NVCC" does? NVCC is the nvidia cuda compiler, maybe it was not found? I found this: CUDA codes runs on

Re: [gmx-users] Density of States syntax question

Hi, Per your suggestion, I uninstalled Gromacs v5.1.2, and installed Gromacs v5.0.1, and re-ran the tutorial (changing from TIP4PEW to TIP4P for simplicity). The tutorial ran fine, but when I tried calculating the dos, I get the following error message:

Re: [gmx-users] Calculating Dielectric constant

On 30/05/16 14:33, Life Sciences Inc wrote: Dear ALL Gromacs users I am trying to calculate Dielectric constant using the option in my simulation file as epsilon-surface = 70 . whenever I try to run the simulaton I get this warning message "Since molecules/charge groups are broken using the

Re: [gmx-users] Calculating Dielectric constant

On 31/05/16 15:26, Life Sciences Inc wrote: Dear Justin I tried to run the simulation by changing cutoff scheme from verlet to group, but its giving error of too many LINCS warnings (1001), Any idea how to fix this issue I have already minimized and equiliberated my structure with nvt for few

Re: [gmx-users] Error while re-compiling Gromacs 5.1.2 with GPU and gcc 5.3.1

Hi, As far as I know cuda 7.5 only supports branch 4.X of gcc, not 5.X ; what about forcing the use of gcc-4.9: CC=gcc-4.9 CXX=g++-4.9 cmake [OTHER FLAGS] .. Regards, Florent Hédin On 31/05/16 19:42, Diogo Martins de Sá wrote: Hi Nikhil, You can get CUDA toolkit 7.5 using apt-get install

Re: [gmx-users] How to generate opls aa parameters for new element myself?

The procedure as I understand is that you need to first edit the OPLSAA files. I found that it worked best if I created a copy of the whole folder. These files are in your installation directory. You'll need to edit the atomname2type.n2t file at a minimum. You'll need to create a type for the Pt

Re: [gmx-users] Error while re-compiling Gromacs 5.1.2 with GPU and gcc 5.3.1

Hi Nikhil, You can get CUDA toolkit 7.5 using apt-get install nvidia-cuda-dev nvidia-cuda-toolkit. Also, if you open the link I've sent, you`ll see the step on how to install directly from provider. NAMD ran with CUDA this way. So it is supported. Installing directly with apt-get gives the same

Re: [gmx-users] trjconv -dump buffer overflow

Hi, It's hard to say. Does it happen with earlier frames? Mark On Mon, May 30, 2016 at 4:33 PM Marlon Sidore wrote: > Dear Gromacs users, > > I'm trying to output frames of my trajectory to individual .gro files and > have been trying to use trjconv -dump (or -sep,

Re: [gmx-users] How to generate opls aa parameters for new element myself?

Hi, I would start the other way around. Review the literature of who has successfully modelled a metal surface plus a peptide, and plan to learn from what they did. It may be clear to use some other software or force field. Mark On Tue, 31 May 2016 06:52 Wang Tao wrote:

Re: [gmx-users] Gromacs 5.1 I/O strategy

Hi, What I/O happens depends very much on how you call mdrun and what your mdp options were. So nobody can be definitive yet. But typically only one rank per simulation writes any I/O, after reducing the data to that rank internally. Mark On Tue, 31 May 2016 09:45 Andreas Mecklenfeld <

Re: [gmx-users] Confusion regarding creation of .itp file

Hi, Chapter 5 is your best friend, particularly table 5.5 (IIRC) Mark On Tue, 31 May 2016 19:10 Nikhil Maroli wrote: > All these available in manual, regarding topology building you can refer > the tutorials and server web pages > > > > -- > Gromacs Users mailing list > >

Re: [gmx-users] Confusion regarding creation of .itp file

All these available in manual, regarding topology building you can refer the tutorials and server web pages -- 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

Re: [gmx-users] [gmx-developers] GTX 680 non detected on OS X

So to summarize: - your installation does have shared libraries (we know); - you set CUDA*USE*STATIC*CUDA*RUNTIME=OFF (which is what the change does and what you can also do manually in cmake) ? - and you are still getting gmx statically linked against libcudart? -- Szilárd On

Re: [gmx-users] Error while re-compiling Gromacs 5.1.2 with GPU and gcc 5.3.1

Hi as per my understanding, CUDA is not supported Ubuntu 16.04 from the provider -- 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 * For

[gmx-users] Angle between a vector and the normal to a sphere

OK thanks Yu, I have another question how to select the water sphere center dynamically With g_select? S - Hi St?phane, gmx gangle may be what you need. http://manual.gromacs.org/programs/gmx-gangle.html -Yu 2016-05-31 13:22 GMT+02:00 ABEL Stephane

[gmx-users] Error while re-compiling Gromacs 5.1.2 with GPU and gcc 5.3.1

Hi guys, I am running kubuntu 16.04 and installed CUDA toolkit 7.5 like was done here: https://www.pugetsystems.com/labs/articles/NVIDIA-CUDA-with-Ubuntu-16-04-beta-on-a-laptop-if-you-just-cannot-wait-775/ I used cmake with the following command line: cmake .. -DGMX_BUILD_OWN_FFTW=ON

[gmx-users] GROMACS 2016-beta2 released

Hi GROMACS users, The second beta release of GROMACS 2016 is available! We are making this available to you to get an early taste of how GROMACS 2016 will look and work, and most importantly to get feedback from you about how well things work. While we try our hardest to keep the quality of

Re: [gmx-users] Density of States syntax question

Hi! That's an bug that was not corrected yet for the 5.1 version. Its somehow linked to a safety measure that went nuts. The issue was already directed to the admins. Try to use 501 version. For me, it works just fine. Cheers! 2016-05-31 10:59 GMT-03:00 Chapman, Christopher W.

[gmx-users] Density of States syntax question

Hello all, I am new to Gromacs, so I apologize if this is a trivial question. I'm running a Gromacs tutorial (found at https://github.com/wesbarnett/gromacs-tutorials/tree/master/1_tip4pew_water) using Gromacs v5.1.2, and I was trying to get the Density of States from the production run. When

Re: [gmx-users] Calculating Dielectric constant

Dear Justin I tried to run the simulation by changing cutoff scheme from verlet to group, but its giving error of too many LINCS warnings (1001), Any idea how to fix this issue I have already minimized and equiliberated my structure with nvt for few ps and npt for 5ns. Thanks On Mon, May 30,

Re: [gmx-users] [gmx-developers] GTX 680 non detected on OS X

uliano@MacPro:~$ ls /Developer/NVIDIA/CUDA-7.5/lib libcublas.7.5.dylib libcusolver_static.a libcublas.dylib libcusparse.7.5.dylib libcublas_device.a libcusparse.dylib libcublas_static.a libcusparse_static.a libcudadevrt.a libnppc.7.5.dylib

Re: [gmx-users] Angle between a vector and the normal to a sphere

Hi Stéphane, gmx gangle may be what you need. http://manual.gromacs.org/programs/gmx-gangle.html -Yu 2016-05-31 13:22 GMT+02:00 ABEL Stephane 175950 : > Hi all, > > Is there a command/tool in a gromacs to compute the angle between a vector > defined defined two atoms

Re: [gmx-users] [gmx-developers] GTX 680 non detected on OS X

OK, but if all you have is static libraries, then that is all that CMake can do, which is why I asked whether you have shared libraries where CMake can find them? Mark On Tue, May 31, 2016 at 2:39 PM Uliano Guerrini wrote: > Hi Mark, > > the patch was active, in the

Re: [gmx-users] [gmx-developers] GTX 680 non detected on OS X

Hi Mark, the patch was active, in the sense that I pasted the 3 lines if (APPLE)… in between of the corresponding location (not same lines) of the relevant file of gramacs 5.1.2. I recompiled now without any difference (libcudart always static). uliano > On 31 May 2016, at 11:31, Mark

[gmx-users] Confusion regarding creation of .itp file

Hello, I'm a beginner in GROMACS and have been trying to process small molecule topologies through GROMACS for quite sometime. Initially while adding new residues , I thought it's better to modify forcefield files such as ffnonbonded.itp, residuetypes.dat, .rtp entries. However, I've seen in many

[gmx-users] Angle between a vector and the normal to a sphere

Hi all, Is there a command/tool in a gromacs to compute the angle between a vector defined defined two atoms molecule and the normal to a sphere defined by a set of atoms for instance water ? if yes, how I use a version of gromacs > 5.0 Thanks Stéphane -- Gromacs Users mailing list *

Re: [gmx-users] [gmx-developers] GTX 680 non detected on OS X

Hi, The point of the patch that I linked was to specifically disable static linking in what sounds like your case. What linking resulted from it? Do you even have shared libraries installed? What does NVIDIA do/recommend on Mac? Mark On Tue, 31 May 2016 11:25 Uliano Guerrini

Re: [gmx-users] [gmx-developers] GTX 680 non detected on OS X

> > The output you pasted into that email clearly shows that libcudart is > *statically* linked, so it's normal that it does not show up in the otool > output (you can list the symbols in your binary with some OS X tool similar > to nm if you want to verify). > > I have *no Idea* of the

[gmx-users] Gromacs 5.1 I/O strategy

Dear Gromacs-users, I'm currently working on a project proposal to acquire computational time. For this, I have to specify the I/O strategy used in Gromacs 5.1. Unfortunately, I found very little information about this topic. By analyzing my log-files, it seems that all (12) MPI ranks