Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 183, Issue 27 convergence of bilayer simulation

Hi Prasanth, There are lots of thermodynamic parameters you can check to see if your bilayer simulation has converged or not, but I would check the convergence of RMSD. Best regards -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Install on Windows 10 with AMD GPU

I suspect the issue is that 64bit OpenCL is required and 32bit is enabled by default on this card. Apparently I can somewhere set GPU_FORCE_64BIT_PTR=1 But no idea how to do this yet... -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se On Behalf Of Szilárd

[gmx-users] convergence of bilayer simulation

Dear all, I am carrying out a simulation to equilibrate lipid bilayer (POPC) in water, which I would like to use for membrane protein simulation. Is there a way to know, if a lipid bilayer simulation has converged or not? -- Regards, Prasanth. -- Gromacs Users mailing list * Please search the

Re: [gmx-users] missing prepare-qmmm.py

Thanks. On 7/10/19 2:38 PM, Dhr. D.W. Sjoerdsma (d.w.sjoerdsma) wrote: Dear Benson, Thank you for all the time you put in! I'll try one of these guys and share the updates! Sincerely, Derk Sjoerdsma On July 10, 2019 at 12:54 PM Benson Muite wrote: Dear Derk, Ok. Got the same result.

Re: [gmx-users] acpype error

Do you have the charges set inside your mol2 file? Which acpype version are you using? Be sure to be using the latest, which you can get by: git clone https://github.com/alanwilter/acpype.git If still having problems, please run: acpype -di ligand.mol2 -c user # -d is for debug mode and send

[gmx-users] acpype error

I installed acpype to generate the necessary files of  ligand.if I use this command: "Acpype -i ligand.mol2 -c user" I will get following message:"ACPYPE FAILED: [Errno 2] No such file or directory: 'tmp'" Please guide meThanks a lot -- Gromacs Users mailing list * Please search the

Re: [gmx-users] missing prepare-qmmm.py

Dear Derk, Ok. Got the same result. Perhaps contact one of the main authors of the following papers: Extreme Scalability of DFT-Based QM/MM MD Simulations Using MiMiC by Viacheslav Bolnykh et al https://doi.org/10.26434/chemrxiv.8067527.v1 MiMiC: A Novel Framework for Multiscale Modeling

Re: [gmx-users] missing prepare-qmmm.py

Dear Benson, Thank you for your reply :) I indeed set the -DCMAKE_PREFIX_PATH flag correctly. I also looked what the syntax of the -DCMAKE_INSTALL_PREFIX was. However after trying the correct syntax, I still was not able to get the prepare-QMMM.py It should however be generated as is said in

Re: [gmx-users] Tetrahedral order

Thanks Sir, But it is giving the xpm file. How can I get xvg file? On Wed, Jul 10, 2019, 06:51 Justin Lemkul wrote: > > > On 7/9/19 4:24 AM, Omkar Singh wrote: > > Dear all, > > I want to calculate the Tetrahedral order parameter through gmx. Can > anyone > > help? Eventhough I tried but my

Re: [gmx-users] How to let mdrun not generate trr file

Remove velocity saving settings from mdp file.Sent using Zoho Mail On Tue, 09 Jul 2019 20:48:40 +0530 sunyeping wrote Hello everyone, "gmx mdrun -dffname md_0_1" will generate all production files including .trr, .xtc, .cpt, .log, etc.. If I don't want

Re: [gmx-users] what's the maximum number of atoms that GROMACS can simulate?

Hello Carsten, Thanks for your reply! The system I'm testing is a 128x128x128 nm box containing only water. I tried using double precision, but the error is the same. There are lots of errors like this: Program: gmx mdrun, version 2019.3 Source file: src/gromacs/mdlib/nbnxn_grid.cpp (line

Re: [gmx-users] rtx 2080 gpu

Hi Stefano, What was your compilation command? (it may be helpful to add SIMD support appropriate to your processor http://manual.gromacs.org/documentation/current/install-guide/index.html#simd-support) Did you run make test after compiling? Benson On 7/10/19 1:18 AM, Stefano Guglielmo

Re: [gmx-users] make test failed during installing gromacs

Hi Yeping, a) Would first check that a CPU only build passes the tests. b) May then want to check compute capability of GPU matches the requirements for the Gromacs version you are installing. I assume using Geforce GTX 1080 GPU It may be helpful to indicate your compilation commands and