Re: [gmx-users] GMX Error after CUDA update

Dear Mark, Thank you for the answer. I was afraid that this is the only possibility to fix it. Best, Krzysztof czw., 21 cze 2018 o 23:00 Mark Abraham napisał(a): > Hi, > > Rolling distros tend to have only one version of things available, leading > to symptoms as you describe, for which the

Re: [gmx-users] GMX Error after CUDA update

Hi, Rolling distros tend to have only one version of things available, leading to symptoms as you describe, for which the remedy is to recompile. Mark On Thu, Jun 21, 2018 at 10:54 PM Krzysztof Kolman < krzysztof.kol...@gmail.com> wrote: > Dear Gromacs Users, > > After my system update

[gmx-users] GMX Error after CUDA update

Dear Gromacs Users, After my system update (Manjaro), I can not run Gromacs anymore. I noticed that Cuda has been update from version 9.1 to 9.2 and now I get following error: gmx: error while loading shared libraries: libcufft.so.9.1: cannot open shared object file: No such file or directory Is

Re: [gmx-users] Magnetic field in GROMACS

Dear Alex, Thanks for your words. Yes, we have going on research and we look to the future. But we are suffering from the lack of resources. We did some work on electric field code but we could not call the velocity of each particle to do the cross product with the magnetic field and also our

Re: [gmx-users] how to improve computing?

Szilárd, I attached .log file. Can does it mean I can use two graphic cards with this processor to improve calculation? Best regards,Vlad 14.06.2018, 18:14, "Szilárd Páll" :Vlad,Please share your log file(s), it's easier to be concrete about a concrete case.mdrun will by default attempt to use all

Re: [gmx-users] GTX 960 vs Tesla K40

On Mon, Jun 18, 2018 at 11:35 PM Alex wrote: > Persistence is enabled so I don't have to overclock again. Sure, makes sense. Note that strictly speaking this is not an "overclock", but a manual "boost clock" (to use terminology CPU vendors use). Consumer GPUs automatically scale their clock

Re: [gmx-users] Dihedrals/Impropers

On 6/21/18 10:22 AM, Salman Zarrini wrote: Dear all, I wonder if it is necessary to list all the Dihedrals/Impropers of the molecule in a MD simulation? If not so, what kind of Dihedrals we don't need to list? The topology needs to contain every interaction that's relevant. Nothing is

[gmx-users] Dihedrals/Impropers

Dear all, I wonder if it is necessary to list all the Dihedrals/Impropers of the molecule in a MD simulation? If not so, what kind of Dihedrals we don't need to list? Thank you. Regards, Salman -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Deuterium atoms

Typically, deuterium is treated with the same parameters as H, but with double the mass. Most papers don't even bother with the re-parameterization, using the argument that the bond-lengths will not change substantially. Instead the authors focus on how the dynamics are slowed. If you really

Re: [gmx-users] Deuterium atoms

On 6/21/18 9:05 AM, Hermann, Johannes wrote: Hello Justin, okay that is beyond my expertise. Do you know / think if there will be a force field in the future where deuterium is present? There are tons of published studies that have done MD with deuterium. I suggest you start there.

Re: [gmx-users] Deuterium atoms

Hello Justin, okay that is beyond my expertise. Do you know / think if there will be a force field in the future where deuterium is present? All the best Johannes On 21.06.2018 15:01, Justin Lemkul wrote: On 6/21/18 8:53 AM, Hermann, Johannes wrote: Hello Justin, thank you for your

Re: [gmx-users] Deuterium atoms

On 6/21/18 8:53 AM, Hermann, Johannes wrote: Hello Justin, thank you for your answer. So the only way to simulate with deuterium atoms would be a parametrization of the force field, in particular the bonded force constant? At minimum. All parameters are connected, so angles and

Re: [gmx-users] Deuterium atoms

Hello Justin, thank you for your answer. So the only way to simulate with deuterium atoms would be a parametrization of the force field, in particular the bonded force constant? Thank you in advance! All the best Johannes On 21.06.2018 14:16, Justin Lemkul wrote: On 6/21/18 3:47 AM,

[gmx-users] Implicit solvent

: > I want to perform MD simulation using groamcs in implicit solvent. Can you > help me which force field is compatible with which solvent I can take? > > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

[gmx-users] fatal error with mpi

Dear users, I have installed gromacs with MPI instead of its native tMPI and I am encountering the following error: "Fatal error: 4 particles communicated to PME rank 5 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension y. This usually

Re: [gmx-users] No line with moleculetype 'SOL' found the [ molecules ] section

Dear Justin, Thank you for your suggestion. I have solved the problem! C. -Mensaje original- De: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] En nombre de Justin Lemkul Enviado el: jueves, 21 de junio de 2018 1:11 Para:

Re: [gmx-users] opnempi

Thanks, I did it 2018-06-21 1:08 GMT+02:00 Benson Muite : > Hi, > > Might try using ccmake to get user interface and check variables are setup > correctly. > > Regards, > Benson > > On 06/21/2018 02:03 AM, Stefano Guglielmo wrote: > >> Dear gromacs users, >> >> I am trying to compile gromacs

Re: [gmx-users] Continuation of the gromacs job using gmx convert-tpr

On 6/21/18 2:35 AM, Own 12121325 wrote: and without append flag it will produce an output in the separate file, won't it? No, because appending is the default behavior. Specifying -append just invokes what mdrun does on its own. If you want a separate file, add -noappend to your mdrun

Re: [gmx-users] Deuterium atoms

On 6/21/18 3:47 AM, Hermann, Johannes wrote: Thanks Vytautas, might solve it! And additionally change the mass in the force field. Increasing the mass will also change the vibrational frequency of any bonds involved, requiring a reparametrization of the bonded force constant. If you're

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

A quick update. FFTW is supposed to create fat binaries and ignore the AVX that it cannot use. Regardless, this did not happen the right way. I've modified the src/contrib/fftw/CMakeFiles/fftwBuild.dir/build.make and removed the --enable- "512avx" and other terms and this removed the issue.

[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.

Re: [gmx-users] Magnetic field in GROMACS

I would at least first try to hardcode a test Lorentz force for e.g. a given constant magnetic field to see what happens and whether you can observe anything fun. On an unrelated note, I just want to say that it is great to see that there is scientific research going on in Iraq after years of

Re: [gmx-users] Magnetic field in GROMACS

I thought you are a developer ;) I think updating electric field file is not a problem but the complicated thing is what are the other files that related to it. Such as how to implement it in mdp files which I think need to update different files. If there are any analyzing commands need updating,

Re: [gmx-users] S-nitrosoylated proteins

I suggest to check this one: Han S. Force field parameters for S-nitrosocysteine and molecular dynamics simulations of S-nitrosated thioredoxin. Biochem Biophys Res Commun. 2008 Dec 12;377(2):612-616. doi: 10.1016/j.bbrc.2008.10.017. Epub 2008 Oct 16. PubMed PMID: 18929538. On Wednesday,

Re: [gmx-users] Deuterium atoms

Thanks Vytautas, might solve it! And additionally change the mass in the force field. On 21.06.2018 09:24, Vytautas Rakeviius wrote: Just change all D to H in structure file IMHO. On Wednesday, June 20, 2018, 5:39:18 PM GMT+3, Hermann, Johannes wrote: Dear all, is there any

Re: [gmx-users] Deuterium atoms

Just change all D to H in structure file IMHO. On Wednesday, June 20, 2018, 5:39:18 PM GMT+3, Hermann, Johannes wrote: Dear all, is there any force field in gromacs (or elsewhere) which can handle deuterium atoms? All the best Johannes -- __

Re: [gmx-users] Magnetic field in GROMACS

Nah, I'm just a user. ;) What David and I were discussing is not a beginner's task (and I can't see a large number of users for that otherwise awesome functionality), but if you'd like to code the simple vector product, I am pretty sure there will be those who could direct you to the right

Re: [gmx-users] Magnetic field in GROMACS

Dear David and Alex, Thanks for the replies. I'm happy that you will consider it. You are the developers and it is clear for you which file should be updated; Dear Ali, My coding skills are very bad and I have no idea which file I need to look at. Best On Wed, Jun 20, 2018 at 12:02 PM, Ali

Re: [gmx-users] Continuation of the gromacs job using gmx convert-tpr

and without append flag it will produce an output in the separate file, won't it? gmx convert-tpr -s init.tpr -o next.tpr -extend 50 gmx mdrun -s next.tpr -cpi the_last_chekpoint.cpt 2018-06-21 1:12 GMT+02:00 Justin Lemkul : > > > On 6/19/18 4:45 AM, Own 12121325 wrote: > >> Hello Justin,

Re: [gmx-users] (no subject)

Also depends on what you try to do. Maybe Dry Martini? Look into:ARNAREZ, Clément, et al. Dry Martini, a coarse-grained force field for lipid membrane simulations with implicit solvent. Journal of chemical theory and computation, 2014, 11.1: 260-275. On Thursday, June 21, 2018, 5:22:15