Re: [gmx-users] Gromac4.6.7 installation problem

Hi, For the record, with GROMACS 4.6.7, the gcc 5.4.0 in ubuntu 16.04.2 with CUDA 8.0 installed and past tests perfectly for me on a 24-core AMD dual-GPU node, with and without the own-fftw option. So something about your machine looks fishy. You should not need to provide linker flags, but they

Re: [gmx-users] linking error while trying to build gromacs

Hi, That's a cmake log for a different run (building fftw via GROMACS vs not). But I can build and install the 5.1.4 tarball fine with the stock gcc 5.4.0 on ubuntu 16.04.02 and cuda 8.0, with or without building ffftw via GROMACS. Mark On Fri, Mar 3, 2017 at 9:26 PM Толстов Андрей

Re: [gmx-users] Analyzing Desmond trajectories using GROMACS tools

On 3/3/17 11:28 AM, zeineb SI CHAIB wrote: Dear gmx users, I'm running simulations on membrane proteins (POPC) using Desmond software and I would like to use GROMACS tools to analyze certain parameters related to the membrane. Exemple: - Deuterium order parameters of the acyl chains -

Re: [gmx-users] linking error while trying to build gromacs

HI, Thanks for yuor reply. Here is log of my cmake output. I can't find anything significantly wrong there. Andrey 03.03.2017, 10:39, "Mark Abraham" :Hi,The simplest explanation would be that your C compiler and your C++compiler are somehow incompatible. But we'd have to

Re: [gmx-users] Gromac4.6.7 installation problem

Hi, So that means your gcc 4.9 works, but something about the cuda or build system doesn't work right in such an old (and slow) version of Gromacs. Ubuntu 16.04 ships a new version of glibc which could also be a problem. The error is probably not a problem, but we would be interested to see

Re: [gmx-users] Gromac4.6.7 installation problem

Thanks Mark. I tried gcc 4.9 and used it as follows: cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=ON -DCMAKE_INSTALL_PREFIX=/home/mohsen/programs-mohsen -DCMAKE_CXX_LINK_FLAGS="-Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/4.9 -L/usr/lib/gcc/x86_64-linux-gnu/4.9" I tried

Re: [gmx-users] Dihedral PCA documentation

Sorry for the delay, but I wanted to add a few points to this discussion as I am doing my PhD in the group where dPCA was developed. I hope these will clarify a little bit what's done in the tutorial and why (took me a while to figure it out). Obviously, it would be worth to rewrite my comments in

[gmx-users] Analyzing Desmond trajectories using GROMACS tools

Dear gmx users, I'm running simulations on membrane proteins (POPC) using Desmond software and I would like to use GROMACS tools to analyze certain parameters related to the membrane. Exemple: - Deuterium order parameters of the acyl chains - Density of the membrane environment - Area per lipid

Re: [gmx-users] Velocity as a function of distance Z

On Fri, Mar 3, 2017 at 11:50 AM Kamps, M. wrote: > (previous mail was sent prematurely, my apologies) > > Dear Mark, > > Again, thanks for the reply. > > You said I should identify groups of molecules that are to my > interest. I'm unsure how to do this. > My .gro files

Re: [gmx-users] Distance between centers of mass

On 3/3/17 5:38 AM, CROUZY Serge 119222 wrote: Hi Justin Bouncing back on your early answer about gmx distance, I noticed something strange (to me) I'musing the same instruction for a protein file prot.gro gmx distance ... -select "com of group 'Protein' plus com of group 'Ligand'" and

Re: [gmx-users] CGenFF generated prm/itp overriding and messing with charmm36-nov2016.ff?

On 3/2/17 11:28 PM, Jonathan Saboury wrote: I think I narrowed it down to the problem. This time I only simulated MIY in water and the problem occurs in gmx solvate and gmx grompp gmx solvate seems to only reads a max of 3 chars for atom type/number (not sure the correct name, it is the 3rd

Re: [gmx-users] Invalid Order for Directive Defaults Error Due to Force Field Mixing

On 3/3/17 1:49 AM, Amir Zeb wrote: Hi Dr. Justin, I'm wondering that you have mentioned CHARMm27 is not a valid identifier of protein forcefield, but we have so many articles already published while using CHARMm27 ff. Can you please let us know how to trace this unsuitability of CHARMm27

Re: [gmx-users] Per lipid area for heterogeneous membrane

On 3/2/17 11:31 PM, Мижээ Батсайхан wrote: Dear Justin, Thank you very much. I analyzed 1001 frames of trajectory. All outputs are written in separate files. How can I summarize over all time? They're all just plain text files, so use any scripting language you like to compile the

Re: [gmx-users] Updating/upgrading GROMACS

Hi Szilárd, Many thanks for the idea to keep the multiple versions! Gregory On 3/2/17 2:22 PM, Szilárd Páll wrote: Hi Gregory, If you have installed in the default system location, you definitely should clean up before you install a new version (if you did not change the default path, you

Re: [gmx-users] Velocity as a function of distance Z

(previous mail was sent prematurely, my apologies) Dear Mark, Again, thanks for the reply. You said I should identify groups of molecules that are to my interest. I'm unsure how to do this. My .gro files show no distinction between different molecules, all of them are built the same (rows

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 155, Issue 21

Dear Mark, Again, thanks for the reply. You said I should identify groups of molecules that are to my interest. I'm unsure how to do this. My .gro files show no distinction between different molecules, all of them are built the same (rows deleted for clarification). 1EthBC1 5963 18.910

Re: [gmx-users] Distance between centers of mass

Hi Justin Bouncing back on your early answer about gmx distance, I noticed something strange (to me) I'musing the same instruction for a protein file prot.gro gmx distance ... -select "com of group 'Protein' plus com of group 'Ligand'" and now I'm running umbrella sampling with pull code

Re: [gmx-users] Simulation crashes: issue with [pair] potential

Dear Mark, I will go for version 5.1.4 test whether the pairs_nb statement is valid. Thanks for you help and let me report to you soon. Adolfo > Hi, > > When you're using a version of the software that's more than three years > old, and a bug was fixed less than two years ago, you need to get an

Re: [gmx-users] Gromacs with Plumed

Hi, thanks Szilárd for the comment. About changing the version string, which would be the right place to do it in the code? About the last point, do you mean that we should try to put our code into gromacs main trunk? This would be very nice for us (plumed developers), and we discussed several