Re: [gmx-users] problem compiling gromacs 5.1

Hi, The purpose of using a wrapper compiler is that it handles linking all the right stuff. MPI_LIBRARY was a thing from a cmake module we used only in Gromacs 4.5, before we removed it when we decided that wrapper compilers do a better job. So there's nothing that replaces it. That the recent ins

Re: [gmx-users] compressed tng file

Hi, I suspect there's no ability to actually write compressed velocities from mdrun, unless -o .tng defaults to gzip for velocities within libtng (and that won't give a factor of three). I suspect it could be added readily, but it's a question of what needs exist and how to express them in new mdp

Re: [gmx-users] Viscosity calculation by g_tcaf

On Sat, Oct 24, 2015 at 5:31 AM, Pallavi Banerjee < pallavis...@students.iiserpune.ac.in> wrote: > Hello Users, > > Does the viscosity obtained from g_tcaf depend on the system size or the > interval of recording trajectory or both? What is considered to be the > ideal frequency of recording frame

Re: [gmx-users] Segmentation fault in some windows of umbrella sampling

Also I tried the run these windows by using different computers and different Gromacs versions (5.0 and 5.1) however I always got the same segmentation fault error. On Sat, Oct 24, 2015 at 6:37 PM, gozde ergin wrote: > Hi Justin, > > It is totally random. My system is 50 1-decanol2,4,8trimethyl

Re: [gmx-users] problem compiling gromacs 5.1

For 4.6.7 gromacs MPI_Library flag was necessary as well as for 4.5.5. What I am asking here is not weather my admins are doing a good job,and also as you know some things you just got with machine,and sometimes things are not great,so you have to make a workaround. What I am asking here is what is

Re: [gmx-users] compressed tng file

On 24/10/15 21:53, Ahmet Yıldırım wrote: nstxout-compressed = 20 compressed-x-precision = 1000 compressed-x-grps= System Those mdp options will compress only coordinates in the tng file with -x flag. But I want to compress both coordinates and velocities in the tng file with -o o

Re: [gmx-users] compressed tng file

nstxout-compressed = 20 compressed-x-precision = 1000 compressed-x-grps= System Those mdp options will compress only coordinates in the tng file with -x flag. But I want to compress both coordinates and velocities in the tng file with -o option. It seems that GROMACS 5.1 doesn't do

Re: [gmx-users] compressed tng file

Hi, On Sat, Oct 24, 2015 at 9:17 PM David van der Spoel wrote: > On 24/10/15 21:10, Mark Abraham wrote: > > Hi, > > > > I forget the details, but why are you supposing a factor of three? The > best > > you can do with storing full-precision trajectory information to -o .tng > is > > gzip compres

Re: [gmx-users] compressed tng file

On 24/10/15 21:10, Mark Abraham wrote: Hi, I forget the details, but why are you supposing a factor of three? The best you can do with storing full-precision trajectory information to -o .tng is gzip compression, which is well known not to be great for MD trajectories. -x .tng is another matter.

Re: [gmx-users] compressed tng file

Hi, I forget the details, but why are you supposing a factor of three? The best you can do with storing full-precision trajectory information to -o .tng is gzip compression, which is well known not to be great for MD trajectories. -x .tng is another matter. Mark On Sat, Oct 24, 2015 at 8:24 PM A

Re: [gmx-users] problem compiling gromacs 5.1

Hi, On Sat, Oct 24, 2015 at 8:22 PM Ana Marija wrote: > so I managed to install gromacs via: > > #in ams@login1:/lustre/beagle2/ams/new/gromacs/gromacs-5.1/build> > > cmake .. -DFFTWF_INCLUDE_DIR=/opt/fftw/3.3.4.0/abudhabi/include > -DFFTWF_LIBRARY=/opt/fftw/3.3.4.0/abudhabi/lib/libfftw3f.a > -D

[gmx-users] compressed tng file

Dear users, In order to get the tng file smaller than trr file I am using the following command but I get the same file size as trr file. Whereas the tng file file should be about 3 times smaller than the trr file. I wonder if anybody has any clue what's wrong? gmx_d mdrun -v -s md.tpr -cpo md.c

Re: [gmx-users] problem compiling gromacs 5.1

so I managed to install gromacs via: #in ams@login1:/lustre/beagle2/ams/new/gromacs/gromacs-5.1/build> cmake .. -DFFTWF_INCLUDE_DIR=/opt/fftw/3.3.4.0/abudhabi/include -DFFTWF_LIBRARY=/opt/fftw/3.3.4.0/abudhabi/lib/libfftw3f.a -DMPI_LIBRARY="/opt/cray/mpt/7.0.5/gni/mpich2-gnu/49/lib/libmpich.a;/op

Re: [gmx-users] Segmentation fault in some windows of umbrella sampling

Hi Justin, It is totally random. My system is 50 1-decanol2,4,8trimethyl molecules covered on 512 water molecules, Before, I did the umbrella sampling by using 1_decanol2468tetramethyl and 1-decanol as organic molecules and I did not get any error like this. Do you have any idea? Bests On Fri,

Re: [gmx-users] problem compiling gromacs 5.1

Hi, That one's our fault, sorry :-( It'll be fixed in 5.1.1 out shortly, but you can work around it by adding -DSPHINX_EXECUTABLE=no to your cmake call (which, by the way, still has a lot of stuff in it that I've said you don't want to have) Mark On Sat, Oct 24, 2015 at 6:14 PM Ana Marija wro

[gmx-users] problem compiling gromacs 5.1

HI, I tried to configure gromacs 5.1 via: ams@login1:/lustre/beagle2/ams/new/gromacs/gromacs-5.1/build> cmake .. -DFFTWF_INCLUDE_DIR=/opt/fftw/3.3.4.0/abudhabi/include -DFFTWF_LIBRARY=/opt/fftw/3.3.4.0/abudhabi/lib/libfftw3f.a -DMPI_LIBRARY="/opt/cray/mpt/7.0.5/gni/mpich2-gnu/49/lib/libmpich.a;/o

[gmx-users] Viscosity calculation by g_tcaf

Hello Users, Does the viscosity obtained from g_tcaf depend on the system size or the interval of recording trajectory or both? What is considered to be the ideal frequency of recording frames in order to use g_tcaf? Thanks in advance! -Pallavi Banerjee -- Gromacs Users mailing list * Please s