[gmx-users] with 5.0: file INSTALL cannot find gmx

done -- Generating done -- Build files have been written to: /home/waxs/opt/gmx/5.03-rotmax -- --- Dr. Jochen Hub Computational Molecular Biophysics Group Institute for Microbiology and Genetics Georg-August-University of Göttingen Justus-von-Liebig

Re: [gmx-users] with 5.0: file INSTALL cannot find gmx

://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- --- Dr. Jochen Hub Computational Molecular Biophysics

Re: [gmx-users] with 5.0: file INSTALL cannot find gmx

. -- --- Dr. Jochen Hub Computational Molecular Biophysics Group Institute for Microbiology and Genetics Georg-August-University of Göttingen Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany. Phone: +49-551-39-14189 http://cmb.bio.uni-goettingen.de

Re: [gmx-users] with 5.0: file INSTALL cannot find gmx

, and let gromacs build its own fftw3 library is better. I don't know if the fftpack code of gromacs is old. May be Location of where you run cmake/CMakeFiles/CMakeError.log will tell a bit more. On Fri, Dec 12, 2014 at 1:24 PM, Jochen Hub j...@gwdg.de wrote: Am 12/12/14 19:07, schrieb Mark

[gmx-users] New web server for setup of membrane simulation systems

Dear MD community, we have set up a web server that automatically sets up membrane simulation systems containing an arbitrary mixture of different lipids. The server, called MemGen (memgen.uni-goettingen.de) is not restricted to a specific set of lipid types, force fields, or MD software.

Re: [gmx-users] PMF using umbrella sampling and Gromacs 5.0

to gmx-users-requ...@gromacs.org. End of gromacs.org_gmx-users Digest, Vol 135, Issue 136 *** -- --- Dr. Jochen Hub Computational Molecular Biophysics Group Institute for Microbiology and Genetics

Re: [gmx-users] bootstrapping of PMF

e PMF profile by > the "$k_{B}T*log[4π(\epsilon)^2]$" factor in which \epsilon is reaction > coordinate? as been mentioned here: > Hub, J. S.; de Groot, B. L.; van der Spoel, D.J. Chem. Theory > Comput.2010,6, 3713-3720 > > Many thanks for your comments in advance. > &g

[gmx-users] Pulling/restraints along the radius of gyration

-- --- Dr. Jochen Hub Computational Molecular Biophysics Group Institute for Microbiology and Genetics Georg-August-University of Göttingen Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany. Phone: +49-551-39-14189 http://cmb.bio.uni-goettingen.de

[gmx-users] Setting up simulation system of a protein-detergent complex

Hi Gromacs users, if you want to set up an MD simulation system of a protein-detergent complex, you can find some helpful scripts and suggestions here: http://cmb.bio.uni-goettingen.de/build_pdc.html Cheers, Jochen -- --- Dr. Jochen Hub

[gmx-users] Strange energy minimization problem with large Martini box

in 2016.3 and 5.13, in single and double precision, with steep and cg integrator. So seems to be a general problem. Did anyone see something similar? Many thanks, Jochen -- --- Dr. Jochen Hub Computational Molecular Biophysics Group Institute

Re: [gmx-users] Heavy atom - hydrogens bond lengths constraints.

Grabarek -- --- Dr. Jochen Hub Computational Molecular Biophysics Group Institute for Microbiology and Genetics Georg-August-University of Göttingen Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany. Phone: +49-551-39-14189 http://cmb.bio.uni

[gmx-users] 2018-beta1: PME/GPU performance question

. #CPU ns/day 484.11 6 119.24 8 150.84 10 159.63 12 171.30 Is this the expected behaviour? Do you know why? Thank you for any hints, Jochen -- --- Dr. Jochen Hub Computational Molecular Biophysics Group Institute for Microbiology

Re: [gmx-users] 2018-beta1: PME/GPU performance question

t of bonded work (relative to the total step time). Does CHARMM36 use UB? Cheers, -- Szilárd On Thu, Nov 30, 2017 at 5:33 PM, Jochen Hub <j...@gwdg.de> wrote: Dear all, I have a question on the performance of the new PME-on-GPU code (2018-beta1) on a Xeon 12-core / GTX 1080 node (Cuda 8, gcc 4.85).

[gmx-users] AMBER ff14 RNA force field

Hi all, does anyone know if the recent AMBER ff14 RNA force field by Tana, Piana, Dirks, and Shaw is available for download (www.pnas.org/cgi/doi/10.1073/pnas.1713027115)? Google does not find anything. Many thanks, Jochen -- --- Dr. Jochen

Re: [gmx-users] Umbrella Sampling - good histogram but no result in profile

ys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- --- Dr. Jochen Hub Computational Molecular Biophysics Group Institute for Microbiology and Genetics Georg-August-University of Göttingen Justus-von-

Re: [gmx-users] Number of Xeon cores per GTX 1080Ti

Am 03.04.18 um 19:03 schrieb Szilárd Páll: On Tue, Apr 3, 2018 at 5:10 PM, Jochen Hub <j...@gwdg.de> wrote: Am 03.04.18 um 16:26 schrieb Szilárd Páll: On Tue, Apr 3, 2018 at 3:41 PM, Jochen Hub <j...@gwdg.de> wrote: benchmar Am 29.03.18 um 20:57 schrieb Szilárd Páll:

Re: [gmx-users] gmx wham (again)

reaction coordinate is probably fine (using pull_coord1_geometry = direction or direction-periodic). I hope this helped. Cheers, Jochen Would you believe the results obtained this way, assuming otherwise proper setup? Thanks, Alex -- ------

[gmx-users] Number of Xeon cores per GTX 1080Ti

-- --- Dr. Jochen Hub Computational Molecular Biophysics Group Institute for Microbiology and Genetics Georg-August-University of Göttingen Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany. Phone: +49-551-39-14189 http://cmb.bio.uni-goettingen.de

Re: [gmx-users] Number of Xeon cores per GTX 1080Ti

Am 03.04.18 um 16:26 schrieb Szilárd Páll: On Tue, Apr 3, 2018 at 3:41 PM, Jochen Hub <j...@gwdg.de> wrote: Am 29.03.18 um 20:57 schrieb Szilárd Páll: Hi Jochen, For that particular benchmark I only measured performance with 1,2,4,8,16 cores with a few different kinds of GPUs. It

Re: [gmx-users] Number of Xeon cores per GTX 1080Ti

e-GHz: A 10-core E5-2630v4 with 2.2 GHz would have 22 core-GHz, right? Thanks, Jochen Cheers, -- Szilárd On Wed, Mar 28, 2018 at 4:31 AM, Mark Abraham <mark.j.abra...@gmail.com> wrote: Hi, On Tue, Mar 27, 2018 at 6:43 PM Jochen Hub <j...@gwdg.de> wrote: Dear Gromacs comm

Re: [gmx-users] walls with slab of water

--- ERROR 1 [file topol.top, line 45]: Specified wall atom type W1 is not defined ERROR 2 [file topol.top, line 45]: Specified wall atom type W2 is not defined Thanks, Adriano -- --- Dr. Jochen Hub Computational Molecular

Re: [gmx-users] Fixing the molecule in the centre of the micelle

nstcomm = 1 comm-grps= API DLiPC Thanks, Aleksei -- --- Dr. Jochen Hub Computational Molecular Biophysics Group Institute for Microbiology and Genetics Georg-August-University of Göttingen Justus-von-Liebig-Weg 11

Re: [gmx-users] Non-symmetric PMF across lipid bilayer

re posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- ------- Dr. Jochen Hub Comp

[gmx-users] Detection for best SIMD instructions failed, using SIMD None

-- --- Dr. Jochen Hub Computational Molecular Biophysics Group Institute for Microbiology and Genetics Georg-August-University of Göttingen Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany. Phone: +49-551-39-14189 http://cmb.bio.uni-goettingen.de

Re: [gmx-users] Installation with CUDA on Debian / gcc 6+

Am 01.04.19 um 16:52 schrieb Åke Sandgren: Use a newer version of CUDA? CUDA 10.1 supports GCC 8. On 4/1/19 4:33 PM, Jochen Hub wrote: Hi all, we try to install Gromacs with CUDA support on a Debian system. Cuda complains about the gcc 6.30 naively installed on Debian, since Cuda supports

[gmx-users] Installation with CUDA on Debian / gcc 6+

-- --- Dr. Jochen Hub Computational Molecular Biophysics Group Institute for Microbiology and Genetics Georg-August-University of Göttingen Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany. Phone: +49-551-39-14189 http://cmb.bio.uni-goettingen.de

Re: [gmx-users] Installation with CUDA on Debian / gcc 6+

Hi Mark, Szilárd, and Åke, many thanks for your help, this fully answers our questions. Cheers, Jochen Am 01.04.19 um 18:28 schrieb Szilárd Páll: On Mon, Apr 1, 2019 at 5:08 PM Jochen Hub wrote: Hi Åke, ah, thanks, we had indeed a CUDA 8.0 on our Debian. So we'll try to install CUA 10.1

Re: [gmx-users] OPLS parameters for O2

in electrolytes using OPLS force field. Is there any O2 parameters tested with OPLS AA forcefield? Thanks, SF -- --- Dr. Jochen Hub Computational Molecular Biophysics Group Institute for Microbiology and Genetics Georg-August-University of Göttingen Justus

Re: [gmx-users] wham analysis

precision) Reading file umbrella180.tpr, VERSION 5.1.4 (single precision) Reading file umbrella202.tpr, VERSION 5.1.4 (single precision) I would  appreciate any help Tanks in advance, Negar -- ------- Dr. Jochen Hub Computational Molecular Bio

[gmx-users] Performance with Epyc Rome

-- --- Dr. Jochen Hub Computational Molecular Biophysics Group Institute for Microbiology and Genetics Georg-August-University of Göttingen Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany. Phone: +49-551-39-14189 http://cmb.bio.uni-goettingen.de

Re: [gmx-users] Set up anti parallel membrane system for CompEL simulation

However, is there an easy way to invert one of the membrane protein configurations along with the membrane, water and ions? You could try: gmx editconf -rotate 90 0 0 Cheers, Jochen Thanks, Zheng -- --- Prof. Dr. Jochen Hub Theoretical

Re: [gmx-users] Set up anti parallel membrane system for CompEL simulation

Am 04.05.20 um 23:21 schrieb Jochen Hub: Am 04.05.20 um 21:33 schrieb Zheng Ruan: Hi, I'm trying to setup an antiparallel membrane system for CompEL simulation. It is relatively straightforward to convert an existing single membrane system to a parallel system by using # gmx genconf -f

[gmx-users] 2020.1: comm broken with -update gpu -bonded gpu ?

motion removal is broken when doing both *bonded and updating* on the GPU. Is this issue known? Cheers, Jochen -- --- Prof. Dr. Jochen Hub Theoretical Biophysics Group Department of Physics, Saarland University Campus E2 6, Zi. 4.11, 66123

Re: [gmx-users] 2020.1: comm broken with -update gpu -bonded gpu ?

s Lundborg: Hi Jochen, Have you tested if this happens with -update cpu? Perhaps it's the bonded on GPU that's the problem, unrelated to updating. I didn't see a Redmine issue yet. Could you make one? Cheers, Magnus On 2020-03-19 18:01, Jochen Hub wrote: Hi developers, I am running a simple