Re: [gmx-users] failing of g_membed

Hi, As I'm sure you know from reading up on membed, it works by scaling the embedded protein to be tiny and turning off its interactions. The mostly likely issue is that you didn't give those instructions correctly. Double check the documentation, and use a recent version of GROMACS to get the bug

Re: [gmx-users] Gromacs 5.1.4 with GTX 780TI on Ubuntu 16.04; upgraded with GTX1080TI

Hi, You'll get a smooth life if your CUDA driver and runtime are both at least as recent as your device. Your runtime is 8.0 in some cases, and the 384 driver is not very recent. Mark On Wed, Jan 9, 2019 at 1:58 AM paul buscemi wrote: > > > > On Jan 8, 2019, at 6:29 PM, paul buscemi wrote: >

Re: [gmx-users] Shell platform for GROMACS on Windows?

Hi, There's no reason it shouldn't work, but we don't test it. I have heard of reports that setting thread affinity doesn't work with Cygwin, and that will make mdrun slow. Mark On Wed, Jan 9, 2019 at 2:47 AM Neena Susan Eappen < neena.susaneap...@mail.utoronto.ca> wrote: > Thank you Wahab, > >

Re: [gmx-users] How can I install same gromacs on few servers

Hi, If you have a heterogenous cluster and want optimal performance, then you will need multiple GROMACS installations. Doing them on a network shared filesystem and mounting the correct one for each machine is the way to be efficient, but in some cases a local installation on each machine will pe

Re: [gmx-users] REMD Plots

Hi Shan, I am not quite sure if you want to generate an REMD simulation mobility in temperature space for the 30 replicas. If that be the case, then you can use the data in the replica_temperature.xvg file to plot replica index vs REMD steps. The 1st column in the file corresponds to the REMD steps

[gmx-users] Running Replica Exchange with Solute Tempering (REST2) with CHARMM36M

Hello, I am trying to figure out how to run Replica Exchange with Solute Tempering (REST2) simulation using CHARMM 36m force filed. The only method that I found so far involves using Plumed (which would have worked for me). However, the instructions I found ( https://plumed.github.io/doc-v2.4/user

[gmx-users] REMD Plots

Dear Gromacs users, How do we plot a graph for temperature vs swap step number using a REMD simulation with 30 systems. I already generated the replica_temp.xvg and replica_index.xvg files using demux.pl script. Thank you. Best Regards Shan Jayasinghe -- Gromacs Users mailing list * Please sea

Re: [gmx-users] Shell platform for GROMACS on Windows?

Thank you Wahab, Is there any issue with using Cygwin on Windows using GROMACS? Neena From: Neena Susan Eappen Sent: Tuesday, January 8, 2019 4:07 AM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] Shell platform for GROMACS on Windows? He

Re: [gmx-users] Gromacs 5.1.4 with GTX 780TI on Ubuntu 16.04; upgraded with GTX1080TI

> On Jan 8, 2019, at 6:29 PM, paul buscemi wrote: > > I just built from a similar situation but also went to Ubuntu Mint Tara 19 , > cuda runtime 10 ( used the Nvidia web site .run version not the deb - do not > install the driver from the toolkit -- add the 410 driver from the PPA) The

Re: [gmx-users] Gromacs 5.1.4 with GTX 780TI on Ubuntu 16.04; upgraded with GTX1080TI

I just built from a similar situation but also went to Ubuntu Mint Tara 19 , cuda runtime 10 ( used the Nvidia web site .run version not the deb - do not install the driver from the toolkit ) added the 410 driver from the PPA and the system is quite happy. I believe I ran across some informa

Re: [gmx-users] Gromacs 5.1.4 with GTX 780TI on Ubuntu 16.04; upgraded with GTX1080TI

Den 2019-01-08 kl. 20:33, skrev Adarsh V. K.: Dear all, recently upgraded Gromacs 5.1.4 with GTX 780TI on Ubuntu 16.04 with a new GPU GTX1080TI. CUDA from 7.5 to 8. Driver 384. Problem: GPU not detected during MD run. Details are as follows: Try upgrading to gromacs 2019. 1) Running on 1 no

[gmx-users] Gromacs 5.1.4 with GTX 780TI on Ubuntu 16.04; upgraded with GTX1080TI

Dear all, recently upgraded Gromacs 5.1.4 with GTX 780TI on Ubuntu 16.04 with a new GPU GTX1080TI. CUDA from 7.5 to 8. Driver 384. Problem: GPU not detected during MD run. Details are as follows: 1) Running on 1 node with total 8 cores, 8 logical cores, 0 compatible GPUs Hardware detected: But d

[gmx-users] How can I install same gromacs on few servers

Hi, We have few CentOS 7 servers that use the same application stack. I compile Gromacs on one of them and I want to be able to run Gromacs from all of them. I run it from server that Gromacs not compile on it, I got: Illegal instruction What it the best way to install Gromacs for all of them?

[gmx-users] calculate interaction energy between two proteins

hi, i want to calculate interaction energy between two protein. In my system there are two proteins,waters and ions.In my .mdp file the, energygrps = PROTEIN W ION i am using this command gmx energy -f ../dynamic.edr -s ../eq.gro -o ener.xvg then the following options are coming 1 B

Re: [gmx-users] Shell platform for GROMACS on Windows?

On 08.01.2019 05:07, Neena Susan Eappen wrote: > Hello GROMACS users, > To run GROMACS on Windows OS, what is the best shell interface? Cygwin? or > anything else? On Windows, nowadays (Windows 10) GROMACS is either compiled and run: - as a native Windows program through the MS Visual Studio 2

[gmx-users] modified peptide parametrization

Dear Gromacs users, I would like to simulate a protein with a peptidic ligand. However the ligand has modified amino acids such as a phosphothreonine, a naphthyl alanine and a piperidine carboxylic acid. I am not familiar with modified peptide so can anyone guide me toward some webserver such as

[gmx-users] failing of g_membed

Hi All, I have an aligned structure of protein+ligands in the membrane (a mixture of DPPC and DOPC). The structure is solvated with water (gmx solvate -cp protein_ATP_membrane_box.gro -cs -o protein_ATP_membrane_box_solv.gro -p topol1.top) And I used it as input file for g_membed. grompp_d -c prote