Re: [gmx-users] POPC Berger lipids parameters for AMBER99sb

Dear Justin, To use a time step of 4fs(i clicked send by.mistake) On Tue, Jul 9, 2019 at 7:59 AM Carlos Navarro wrote: > Dear Justin, > Thanks for the reply. > I forgot to mention that indeed the reason of using Berger lipids is > because there are united-atom. I'm planning on running computatio

[gmx-users] Tetrahedral order

Dear all, I want to calculate the Tetrahedral order parameter through gmx. Can anyone help? Eventhough I tried but my system has 500 water molecules Fir that I am unable to make index file because it will take lots of time for typing any suggestions. Commend gmx order -f .xtc -s .tpr -b 0 -e 1

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

Hi James, On Mon, Jul 8, 2019 at 10:57 AM James Burchfield < james.burchfi...@sydney.edu.au> wrote: > Thankyou Szilárd, > Headers are available here https://github.com/KhronosGroup/OpenCL-Headers > But I get > CMake Error at cmake/gmxManageOpenCL.cmake:45 (message): > OpenCL is not supported.

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

Hello， I want to know if there is a maximum number of atoms that GROMACS can simulate, or if there are any bugs in the code that cause the error in computing the coordinate of atoms when the number of atoms is very large? I'm trying to simulate some very large systems using GROMACS-2019.3. Unfo

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

Hi Zhang, > On 9. Jul 2019, at 15:16, 张驭洲 wrote: > > Hello， > > I want to know if there is a maximum number of atoms that GROMACS can > simulate, or if there are any bugs in the code that cause the error in > computing the coordinate of atoms when the number of atoms is very large? I'm > try

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

Hello everyone, "gmx mdrun -dffname md_0_1" will generate all production files including .trr, .xtc, .cpt, .log, etc.. If I don't want it to generate .trr file but generate all other file types, how should I write the command? Best regards Yeping Sun -- Gromacs Users mailing list * Please s

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

Hi, If you set nstxout, nstvout and nstfount to zero, then the trr file will have no content. I'm not sure offhand whether that triggers omitting even opening the file... Mark On Tue, 9 Jul 2019 at 17:29, sunyeping wrote: > Hello everyone, > > "gmx mdrun -dffname md_0_1" will generate all prod

[gmx-users] questions about Ryckaert-Bellemans type dihedrals

Hi, I have a question regarding Ryckaert-Bellemans dihedral potentials (function type 3). In the manual of GROMACS 4.5.4 it says to use Ryckaert-Bellemans type, one needs to erase the 1-4 interaction in [pairs] section. My first question is what will happen if I use this potential (type 3) but lea

Re: [gmx-users] Self-interaction across periodic boundaries

Possibly turn pbc off and use nvt PB > On Jul 8, 2019, at 1:31 PM, Salman Zarrini wrote: > > Thanks Mark. > The problem is that I would like to keep the overall concentration > constant, so, using a larger box e.g. with 2 times larger lateral box > dimensions, > needs me to increase the number

[gmx-users] rtx 2080 gpu

Dear all, I have a centOS machine equipped with two RTX 2080 cards, with nvidia drivers 430.2; I installed cuda toolkit 10-1. when executing mdrun the log reported the following message: GROMACS version:2019.2 Precision: single Memory model: 64 bit MPI library:thread_mpi

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

Thanks Szilárd, No difference unfortunately. I wonder if it is due to the new headers files that are no longer version specific. I will see if I can track down an old version -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se On Behalf Of Szilárd Páll Sent: Tue

[gmx-users] make test failed during installing gromacs

Hello, everyone, When I run make test during installing gromacs-2019.3 in centos 7 in a workstation with 4 Tesla 1080 GPU, I get the following failure information: The following tests FAILED: 10 - GpuUtilsUnitTests (Timeout) 38 - MdrunNonIntegratorTests (Timeout) 42 - regressiontests/compl

Re: [gmx-users] POPC Berger lipids parameters for AMBER99sb

On 7/9/19 2:59 AM, Carlos Navarro wrote: Dear Justin, Thanks for the reply. I forgot to mention that indeed the reason of using Berger lipids is because there are united-atom. I'm planning on running computational electrophysiology simulations, and since my system is about 600k atoms I want to

Re: [gmx-users] Tetrahedral order

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 system has 500 water molecules Fir that I am unable to make index file because it will take lots of time for typing any suggestions. Comme

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 env

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 wrot