Re: [gmx-users] GPU performance, regarding

Hi Gromacs, A small digression: Ideally Gromacs would make it more clear in the error message explaining which part is not implemented for the GPUs. Thanks, Mat On Thu, 12 Dec 2019 at 13:01, RAHUL SURESH wrote: > Hi John > > Thank you and adding here the mdp settings > > title =

[gmx-users] 2019.3 - Fixed Issue 2953: With DD, all intermolecular interactions were ignored?

nteractions the most basic interactions that you would expect gromacs to calculate? Regards, Mateusz Bieniek -- 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/S

Re: [gmx-users] Charmm 36m

Yes, the 36m (CHARMM36m) is the new set of parameters recommended by the authors, so it is best to stick to the recommendation unless you know exactly what you are doing. Huang, J. et al., 2016. CHARMM36m: an improved force field for folded and intrinsically disordered proteins. *Nature Methods*,

Re: [gmx-users] Cannot find position restraint file

Hi Neena, The position restraint file is a bit of a new concept. It's the "positions/coordinates" around which the restraints should be applied. That means your posre.itp file was found and requires now the coordinates around which to apply the restraints. Most often people will use their

Re: [gmx-users] Freezing structure's atom

Now I need to freez some atoms that I have their index in a file like > > freez.ndx. How should I change this mdp file? In other word, which > option I > > should add to this file? > > > > Thank you once more, > > Hadi > > > > On Thu, Mar 21, 2019 at 8:42

Re: [gmx-users] Freezing structure's atom

Sent from my iPhone > > > On Mar 20, 2019, at 4:07 PM, Mateusz Bieniek > wrote: > > > > Hi Hadi, > > > > To freeze atoms you have to first create the right group in your index > file > > .ndx. Then, you use this: > > > > freezegrps

Re: [gmx-users] Freezing structure's atom

Hi Hadi, To freeze atoms you have to first create the right group in your index file .ndx. Then, you use this: freezegrps = slab freezedim= Y Y N Where the Ys refer to X Y Z, meaning here the slab group is frozen in X Y dimension but not Z dimension. Please not

Re: [gmx-users] DSSP regardin

Hi Rahul, I've run into a similar issue a year ago. It is possible to configure gmx with the extra configuration file (as described in the documentation) to get this right. However, I found it to be archaic and wrote my own quick DSSP visualiser in matplotlib. I am planning to improve the code

Re: [gmx-users] gmx distance

Hi Andrew, I cannot answer your question about gmx distance but I have been using the MDAnalysis package for this kind of analysis. I am writing this in case you are proficient in python and need more flexibility. The code more or less would look like this: u=MDAnalysis.Universe(gro, xtc) g1 =

Re: [gmx-users] GROMACS- suggestion for GPU buying

Extending this question. I understand that the GPU P100 here has internal CPUs on board. Could Gromacs developer share whether the software is currently capable of using CPUs inside of a GPU? Thanks, Mat On Thu, Jul 12, 2018 at 3:24 PM Szilárd Páll wrote: > If price does not matter, get V100s;

Re: [gmx-users] Making group of different atoms

Hi Chetan, You might consider also using MDAnalysis which has a nice little tool just for this. Here is an example I placed on researchgate: u=MDAnalysis.Universe("filename.gro") selected = u.select_atoms("resid 10-15") selected.write("existing.ndx", mode="a", name="ids10to15") If you don't

Re: [gmx-users] FFTW compiler error: no such instruction

the issue. Thanks, Mat On Thu, Jun 21, 2018 at 11:04 AM Mateusz Bieniek wrote: > Dear Gromacsers, > > After compiling gromacs successfully with SSE4.1 it suggested AVX_256 > instead. With AVX_256 the compilation is interrupted with the FFTW error > below. In this case I am in n

[gmx-users] FFTW compiler error: no such instruction

Dear Gromacsers, After compiling gromacs successfully with SSE4.1 it suggested AVX_256 instead. With AVX_256 the compilation is interrupted with the FFTW error below. In this case I am in need of more CPU power due to the multiple GPUs installed.

[gmx-users] Freezing atoms, energy group exclusion and pressure calculation

I am simulating metallic surface together with proteins and I need to use atom freezing to ensure that the pressure calculation is correct. In the documentation the user is told to use "energy group exclusions" together with freezing atoms. However, the "energygrp-excl" does not work together

Re: [gmx-users] GROMACS 5.1.4 and dssp 2.2.1

I had a similar issue with dssp which suddenly stopped working. Switching to x86 binary worked for me. Linux Arch Mat On Tue, 13 Mar 2018, 09:25 Joe Jordan, wrote: > You can find a dssp binary here http://swift.cmbi.ru.nl/gv/dssp/ > It is also in the ubuntu repo. > You