Re: [gmx-users] umbrella sampling Protein_ligand complex distance calculation

On 1/12/18 7:09 AM, rose rahmani wrote: I had this problem but i couldn't solve it. But i can tell you just a temporary solution; Don't use -sep with trjconv,then use the output conf as an input for gmx distance. it probably gives you sth like this; time distances

Re: [gmx-users] Umbrella sampling-gmx distance

On 1/11/18 11:38 AM, rose rahmani wrote: [ ZnS ] 123456789 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45..

Re: [gmx-users] Converting top or tpr to psf

On 1/11/18 10:24 AM, jamesmkrie...@gmail.com wrote: Thanks Justin. It’s two protein chains, water and NaCl but there are virtual sites and CMAP (charmm27 ff). I generated the full topology with grompp so yes please could I try your script. Would CHARMM-GUI or VMD be able to generate the

Re: [gmx-users] phi/psi

Hi, g_chi has -rama, -phi, and -psi option for this. Ruan On Fri, Jan 12, 2018 at 10:11 AM, João Henriques wrote: > Hello, > > Don't know if there's a native gromacs tool to do so, but I'd use PLUMED > for this sort of thing: >

[gmx-users] Error while compiling GROMACS 2018

Hi, I am trying to install the latest release of GROMACS 2018 on Mac OS X HighSierrra and ran into the following error message. cmake worked without errors so this looks strange. Any help would be appreciated. Greg ygchung@Yongchuls-MacBook-Pro:*~/Desktop/codes/gromacs/build*$ make [ 1%]

Re: [gmx-users] phi/psi

Hello, Don't know if there's a native gromacs tool to do so, but I'd use PLUMED for this sort of thing: https://plumed.github.io/doc-v2.3/user-doc/html/_t_o_r_s_i_o_n.html The last example on that page shows something similar to what you want to do. It's that simple. P.S.: I am not affiliated

[gmx-users] phi/psi

Hi, How to get phi/psi angles from gromacs trajectory file? I used v.4.5.5. best Urszula Urszula Uciechowska PhD University of Gdansk and Medical Univesity of Gdansk Department of Molecular and Cellular Biology ul. Abrahama 58 80-307 Gdańsk Poland

Re: [gmx-users] g_order for all-atom simulations for double bonds

Hi, Regarding g_order/gmx order being incorrect for unsaturated carbons, there is a bug about this (https://redmine.gromacs.org/issues/1166). I would say that I would fix it, but my C/C++ coding isn't good enough to be able to do this properly. Perhaps a warning could/should be issued by the

Re: [gmx-users] umbrella sampling Protein_ligand complex distance calculation

I had this problem but i couldn't solve it. But i can tell you just a temporary solution; Don't use -sep with trjconv,then use the output conf as an input for gmx distance. it probably gives you sth like this; time distances 0.0001.75372870.02386010.0428935

[gmx-users] gmx distance

Hi i'm doing umbella sampling. whenever i use gmx distance after pulling in V.5.1.4 , i wouldn't have proper dist.xvg file. I did what you said Mr.Justin ( as you refered me to this link http://manual.gromacs.org/documentation/2018-latest/user-guide/cmdline.html#g-dist) but still there are some

[gmx-users] NVML library in CUDA 9 & Gromacs 2018

Hi, I have an interesting problem with the NVML library from CUDA 9 (and 9.1) and Gromacs 2018. Namely, the NVML is reported as detected during cmake but Gromacs 2018 is linked without it. This is the cmake command I would issue: m -rf * && CMAKE_PREFIX_PATH=/home/zidar/utils/fftw-3.3.6-gcc/ \