Re: [gmx-users] dssp 3.1.4

Hi, Do check out gmx do_dssp -h and make sure your dssp binary is the right version, with executable permissions, in the right place (or alternatively the appropriate environment variable is set, so that do_dssp can find dssp) Mark On Fri, 1 May 2020 at 18:47, Iman Katouzian wrote: > Good

Re: [gmx-users] Failed to find GROMACS magic number in trr frame header

Hi, No, some kind of breakage, e.g. a filesystem disappeared, or a file transfer was incomplete or the file was edited with some inappropriate tool. Mark On Sat, 18 Apr 2020 at 11:46, Mijiddorj B wrote: > Dear Justin, > > Thank you very much for your reply. I see. However, I have one more >

Re: [gmx-users] Buggy 2020?

Hi, Based on what is in your system, what do you think the behavior should be? A change reflects that one of the versions may be wrong, but not that the new one is necessarily it. Mark On Fri, 10 Apr 2020 at 08:17, Parvez Mh wrote: > Hello All, > > I am wondering if gromacs-2020 is buggy? or

Re: [gmx-users] Concatenating trajectories

... and next time you might be better served by using gmx mdrun -cpi and gmx trjconv -extend so that you have your contiguous trajectory by construction! Mark On Thu., 9 Apr. 2020, 14:17 Qinghua Liao, wrote: > Hello, > > There is an option of -settime for gmx trjcat, with which you can set >

Re: [gmx-users] Per atom energies

Hi, On Sat., 28 Mar. 2020, 04:04 Guilherme Carneiro Queiroz da Silva, < gcarnei...@pos.iq.ufrj.br> wrote: > Hi all, > > I look on google for any answers for such question in this maillist, and I > found related questions but no final answer. > > I wish to compute the heat flux for my system

Re: [gmx-users] compilation error in multidimarray.h

Hi, Intel doesn't supply a standard library, it always gets one from either a gcc or msvc installed on the system. Which versions of gcc libstdc++ are supported varies with the intel version, so you could follow the advice at

Re: [gmx-users] Various questions related to Gromacs performance tuning

Hi, There could certainly be a bug with -ddorder pp_pme, as there's no testing done of that. If you can reproduce with a recent version of GROMACS, please do file a bug report. (Though this week we're moving to new infrastructure, so leave it for a day or two before trying to report it! Mark On

Re: [gmx-users] Failed HardwareTopologyTest on Install (GROMACS 2019.4)

Hi, That's benign, and probably indicates some kind of mismatch in how hwloc was linked (e.g. headers from one version and libraries from another) or compiled (different compiler or version). mdrun will probably say the same thing, but 2019 has fallback code that means you don't need hwloc

Re: [gmx-users] Energy values for 1 step NVT/NVE simulation of 100 water molecules

Hi, That's entirely normal for condensed-phase systems. Negative PE means the system doesn't want to fly apart. Conventionally, zero PE is when every particle is infinitely separated - look at the form of the expression for energy in electrostatics (and gravity) Mark On Wed, 18 Mar 2020 at

Re: [gmx-users] k-space settings in GROMACS

Hi, On Wed, 18 Mar 2020 at 07:02, Anh Vo wrote: > Hi everyone, > > I'm trying to reconstruct in GROMACS some LAMMPS simulation to compare > between the two. I'm simulating a lipid bilayer system with 72 POPC lipids > and 9072 water molecules, as well as a single lipid system (1 POPC > molecule)

Re: [gmx-users] checkpoint files with replica exchange/ -multidir

Hi, On Thu, 12 Mar 2020 at 20:39, Daniel Burns wrote: > Hello, > > I'm using 2 replicas to test exchange conditions. I restarted a run and > included the checkpoint file name (which is identical in each directory > provided under the -multidir option). After the restart, I'm getting 100% >

Re: [gmx-users] Nose-Hoover vs Berendsen vs V-rescale

Hi, It's very likely a good idea to get the velocity distribution right, for the situation you're trying to model. Check out https://www.livecomsjournal.org/article/5957-best-practices-for-foundations-in-molecular-simulations-article-v1-0 (and the other great LiveComsJ material!) Mark On Thu,

Re: [gmx-users] query regarding running simulation using GPU

Hi, Sure. With a GPU-enabled build, you can just continue running almost all kinds of simulations. Mark On Wed, 11 Mar 2020 at 16:33, Snehasis Chatterjee < snehasis.chatterje...@gmail.com> wrote: > Dear Gromacs users, > > I am trying to perform a simulation for a relatively large system using

Re: [gmx-users] Troubleshooting Generic Floating Point Exception Errors

Hi, Depends when you see them. From mdrun, you're generally blowing up (see user guide and FAQ list). From tools, maybe your input data is somehow bad (or bad in part, so try different parts), or you ran into a silent size limitation in the code (see if a smaller data set works and if so file a

Re: [gmx-users] Gromacs 2020

Hi, The code is tested extensively on a range of compilers, so we believe it is correct and compliant. In particular, you're using gcc 6.1.0 and GROMACS tests with 6.4.0, so the issue might have been fixed in the meantime. As newer versions of gcc and cuda will give better performance, I suggest

Re: [gmx-users] Negative Pressure during equilibration

Hi, Check out the GROMACS FAQs - this question is a very frequent one! :-) Mark On Mon, 9 Mar 2020 at 11:42, Sadaf Rani wrote: > Dear Gromacs users > > I am running a free energy test calculation and using position restraints > for all of the system. At the end of pressure equilibration I am

Re: [gmx-users] Automatically assign the protonation states for pdb2gmx

Hi, On Sat, 22 Feb 2020 at 14:07, ZHANG Cheng <272699...@qq.com> wrote: > Thank you Mark! Sorry could you please explain the details of "stdin" of > "pdb2gmx"? Is there a link for it? > The stdin stream is a fundamental concept in how unix terminals work. The echo tool fills that stream for

Re: [gmx-users] Automatically assign the protonation states for pdb2gmx

Hi, Echo works just fine - you just need a way to script what input it injects to the stdin of pdb2gmx. That's logic you need for any solution so is probably easiest. The expect tool may be another option. Mark On Fri., 21 Feb. 2020, 21:41 ZHANG Cheng, <272699...@qq.com> wrote: > I want to run

Re: [gmx-users] gmx trjconv -force option doesn't seem to work.

Hi, Gro format doesn't support fields for forces. Either write out.g96 file, or use gmx traj (better) Mark On Thu., 20 Feb. 2020, 16:43 Justin Lemkul, wrote: > > > On 2/20/20 12:34 AM, 고연주 wrote: > > > > > >Hello! > > > >I have a question about gmx trjconv -force option because it

Re: [gmx-users] Is Gromos force fields not recommended?

Hi, No. Why do you ask? Mark On Tue., 18 Feb. 2020, 01:57 Myunggi Yi, wrote: > Dear users, > > As the same as the title, > > Are Gromos force fields not recommended in Gromacs? > -- > Gromacs Users mailing list > > * Please search the archive at >

Re: [gmx-users] REMD stall out

Hi, That could be caused by configuration of the parallel file system or MPI on your cluster. If only one file descriptor is available per node to an MPI job, then your symptoms are explained. Some kinds of compute jobs follow such a model, so maybe someone optimized something for that. Mark On

Re: [gmx-users] generating Doxygen documentation

Hi, When they succeed, the doxygen targets produce files like $builddir/docs/html/doxygen/html-*/index.xhtml which you can open in your browser. The doxygen for the released versions is on the web however, so it's much easier to just use or refer to that. Mark On Wed, 12 Feb 2020 at 16:30,

Re: [gmx-users] problem with mpi run in REMD simulation

MACS was built, how the job is being run, or how the job is using the GROMACS version. Mark > On Sun, Feb 9, 2020 at 2:30 PM Mark Abraham > wrote: > > > Hi, > > > > First, make sure you can run a normal single-replica simulation with MPI > on > > this

Re: [gmx-users] problem with mpi run in REMD simulation

Hi, First, make sure you can run a normal single-replica simulation with MPI on this machine, so that you know you have the mechanics right. Follow the cluster's documentation for setting up the scripts and calling MPI. I suspect your problem starts here, perhaps with having a suitable working

Re: [gmx-users] T-REMD stalled - no trr files generated

Hi, Sounds like at least one replica isn't stable in its ensemble. Try a multi run without replica exchange and see. Mark On Fri., 24 Jan. 2020, 21:38 Daniel Burns, wrote: > Hi, > > I have a system containing a dimer totaling about 600 residues solvated > with 32,000 water molecules. I have

Re: [gmx-users] Error: Cannot find AVX 512F compiler flag

That tells you what your CPU is capable of. We need to know whether cmake has found the compiler that can issue the instructions. Follow the suggestions Roland and I have made. Mark On Wed, 15 Jan 2020 at 10:45, Shlomit Afgin wrote: > > > I ran: > > cat /proc/cpuinfo | grep -i avx512 > > > >

Re: [gmx-users] Error: Cannot find AVX 512F compiler flag

On Wed, 15 Jan 2020 at 11:07, Tru Huynh wrote: > > gcc is /opt/rh/devtoolset-6/root/usr/bin/gcc > Good, so is Cmake using it? (e.g. remove the build dir and run cmake again to see what it first reports, or inspect $builddir/CMakeCache.txt for the compiler setting) Mark -- Gromacs Users

Re: [gmx-users] Building full GROMACS and mdrun only with MPI and GPU: FFTW and regression tests

Hi, On Fri, 10 Jan 2020 at 10:49, João M. Damas wrote: > Hi all, > > I am trying to build GROMACS in a similar fashion to what is described in > section 2.3.5 of the manual (weblink > < > http://manual.gromacs.org/documentation/2019.5/install-guide/index.html#testing-gromacs-for-correctness >

Re: [gmx-users] The maxwarn fatal errors

Hi, Warnings mean your physics is probably broken, unless you can explain why it isn't. Suggestions for fixing them are in the warnings. Mark On Tue., 7 Jan. 2020, 03:39 변진영, wrote: > Dear everyone, Happy New year! > I have gone through the Justin Lemku tutorial for Umbrella Sampling. >

Re: [gmx-users] Gromax don't recognize -ignh command

Hi, I expect that's a hydrogen in an NH3+ group being added as a terminus to your protein. You might want to tell pdb2gmx to stop trying to help with the termini, with -ter or -noter. Mark On Sun, 29 Dec 2019 at 13:02, ali khamoushi wrote: > Hello everyone > I have PDB file which have

Re: [gmx-users] Gromacs compilation problem

Hi, The fftw build you are trying to do uses gcc by default, and your gcc is so old that AVX512 didn't exist yet, so it cant compile for it. Since you're using the Intel compiler, it's easiest to also use its fft library with cmake -DGMX_BUILD_OWN_FFTW=OFF -DGMX_FFT_LIBRARY=mkl Harder is to

Re: [gmx-users] CO2 virtual site

Hi, On Fri., 20 Dec. 2019, 09:59 Sina Omrani, wrote: > Hi, > I have a problem when I use CO2 model with virtual sites during energy > minimization. I used itp file in the md tutorial and beside the fact that > some of my water molecules can not be settled, I get a positive potential > energy

Re: [gmx-users] Extract LJ-14 energy

Hi, On Thu., 19 Dec. 2019, 18:41 Suvardhan Jonnalagadda, wrote: > Hi All, > > *"GROMACS: VERSION 4.5.5; Precision: single"* > This software is nearly a decade old and is no longer supported. Please update. I have performed an md simulation for 1 time step, on a single molecule > with 17

Re: [gmx-users] Groms 2019.0, simulations using 2 GPUs: RTX 2080Ti

Hi, Yes that's expected. If you want to run two simulations in parallel then you need to follow the advice in the user guide. Two plain calls to gmx mdrun cannot work usefully. Mark On Fri., 13 Dec. 2019, 11:22 Nikhil Maroli, wrote: > Initially, I tried to run 2+ jobs in my workstation with

Re: [gmx-users] Groms 2019.0, simulations using 2 GPUs: RTX 2080Ti

Hi, Those commands are listed in the user guide, please look there :-) Mark On Fri., 13 Dec. 2019, 10:10 Pragati Sharma, wrote: > Hi Paul, > > The option -pme gpu works when I give pme order = 4 in mdp file instead of > 3. but it gives me an increase of 6-7 ns/day. > > @Dave M : I am also

Re: [gmx-users] Can't engage OpenCL (No rule to make target /usr/lib/libOpenCL.so)

Hi, If you use -DOpenCL_LIBRARY then it has to indicate the location of libOpenCL.so because you've short-circuited any attempt to find the library. Check out the advice at http://manual.gromacs.org/documentation/2019/install-guide/index.html#opencl-gpu-acceleration. If you've installed system

Re: [gmx-users] problem of MD simulation

Hi, Look at the log file, mdrun already reported what it was able to detect. For example, if it can't link to the driver at run time then that's where to investigate. Mark On Fri., 13 Dec. 2019, 13:18 Albert, wrote: > Hello, > > I have compiled my Gromacs 2019v3 with the following command

Re: [gmx-users] How to assign PME ranks to particular nodes?

Hi, On Thu., 12 Dec. 2019, 20:27 Marcin Mielniczuk, wrote: > Hi, > > I'm running Gromacs on a heterogenous cluster, with one node > significantly faster than the other. Therefore, I'd like to achieve the > following setup: > * run 2 or 3 PP processes and 1 PME process on the faster node (with a

Re: [gmx-users] GPU performance, regarding

Hi, On Thu, 12 Dec 2019 at 15:03, Paul Buscemi wrote: > What does nvidia-smi tell you? > That won't inform - GROMACS isn't saying it can't find GPUs. It's saying it can't run on them because something Rahul asked for isn't implemented. Mark PB > > > On Dec 12, 2019, at 7:30 AM, John

Re: [gmx-users] GPU performance, regarding

Hi, On Thu, 12 Dec 2019 at 14:35, Mateusz Bieniek wrote: > Hi Gromacs, > > A small digression: Ideally Gromacs would make it more clear in the error > message explaining which part is not implemented for the GPUs. > Indeed, and this case it is supposed to have already written on the log file

Re: [gmx-users] Gromacs 2019.4 compliantion with GPU support

Hi, I suspect that you have multiple versions of hwloc on your system, and somehow the environment is different at cmake time and make time (e.g. different modules loaded?). If so, don't do that. Otherwise, cmake -DGMX_HWLOC=off will work well enough. I've proposed a probably fix for future 2019

Re: [gmx-users] Signal: Floating point exception (8) Signal code: Floating point divide-by-zero (3)

Hi, That sounds very much like a bug, but it's hard to say where it comes from. Can you please open an issue at https://redmine.gromacs.org/ and attach your .tpr files plus a log file from a failing run and the above stack trace? Mark On Thu, 12 Dec 2019 at 08:37, Dave M wrote: > Hi All, > >

Re: [gmx-users] Rigid water constraint forces in trajectory output

Hi, The trajectory forces do not include the constraint forces. You can verify that by comparing them with those from mdrun -rerun from 2019.x, because constraints are not applied in a rerun. Mark On Wed, 11 Dec 2019 at 17:39, Jacob Monroe wrote: > Hi all, > > I'm working on calculating

Re: [gmx-users] configure gmx with external mpi library - an error

; > >Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios > > Karkoulis > > Peter KassonJiri Kraus Carsten Kutzner Per Larsson > >Justin A. LemkulViveca LindahlMagnus Lundborg Erik > Marklund > > > >

Re: [gmx-users] Seg Fault with Gromacs gmx grompp command - Intel compiler

> #8 0x2aaab1039549 in gmx::CommandLineModuleManager::run(int, char**) > () >from /afs/ > cad.njit.edu/linux/gromacs/intel/2019.4/bin/../lib64/libgromacs.so.4 < > http://cad.njit.edu/linux/gromacs/intel/2019.4/lib64/libgromacs.so.4> > #9 0x00407928 in m

Re: [gmx-users] Seg Fault with Gromacs gmx grompp command - Intel compiler

OK, that looks fine. What does the stack trace of the segfault look like? e.g. gdb --args /the/gmx grompp -whatever -args Mark On Fri, 6 Dec 2019 at 15:29, Glenn (Gedaliah) Wolosh wrote: > > > > On Dec 6, 2019, at 9:12 AM, Mark Abraham > wrote: > > > > Hi,

Re: [gmx-users] Seg Fault with Gromacs gmx grompp command - Intel compiler

not available in the environment. Mark On Thu, 5 Dec 2019 at 21:36, Glenn (Gedaliah) Wolosh wrote: > Thanks for the quick response. I do have the environment properly prepare > via modules. > > GW > > > > On Dec 5, 2019, at 3:24 PM, Mark Abraham > wrote: > > &

Re: [gmx-users] The total charge is not integer : -0.00465

Hi, If, for example, you inserted 465 polymer molecules each with charge -.001 then the most appropriate path forward is to make the total charge of each molecule be neutral. But we don't know enough about what you're doing yet. Mark On Thu, 5 Dec 2019 at 23:34, SAKO MIRZAIE wrote: > Dear

Re: [gmx-users] Problem restarting job 2016.4 with gromacs 2019-4

Hi, A checkpoint restart is indeed not supported. But you can be creative with the old version of gromacs e.g. gmx grompp -f -p -c -cpi old.cpt -s new.tpr, and then that .tpr file has the content of the .cpt in a format that the newer gmx will be able to run (unless we actually removed necessary

Re: [gmx-users] Seg Fault with Gromacs gmx grompp command - Intel compiler

Hi, I suspect you need to prepare the intel environment at run time like you did before compilation. Probably you (or a module you loaded) source-d a compilervars.sh file, and that's probably what you need here. Mark On Thu, 5 Dec 2019 at 20:22, Glenn (Gedaliah) Wolosh wrote: > > Also posted

Re: [gmx-users] Gromacs 2019.4 - cudaStreamSynchronize failed issue

Hi, What driver version is reported in the respective log files? Does the error persist if mdrun -notunepme is used? Mark On Mon., 2 Dec. 2019, 21:18 Chenou Zhang, wrote: > Hi Gromacs developers, > > I'm currently running gromacs 2019.4 on our university's HPC cluster. To > fully utilize the

Re: [gmx-users] Segmentation fault using gmx solvent

Hi, gmx solvate shouldn't segfault based on a minor change to the input coordinates, so it's probably a bug to look into. Please open an issue at https://redmine.gromacs.org and attach inputs with a failing gmx command, and someone can likely provide some insight! Mark On Thu, 14 Nov 2019 at

Re: [gmx-users] slurm, gres:gpu, only 1 GPU out of 4 is detected

Hi, gmx can only detect devices that are visible to it. Your use of slurm is making only one device visible, so gmx can't understand what you mean with -gpu_id 1. But you don't need to manage the same thing twice. If gmx can only see one device and --gres won't allocate a previously allocated

Re: [gmx-users] Slurm for GROMACS

Hi, SLURM and OpenMPI do different things. SLURM is a resource manager, from which you might request multiple compute nodes. OpenMPI is a parallelism library that allows a program to run on those nodes. GROMACS is the program, and it doesn't care which MPI library is in use, or which resource

Re: [gmx-users] Getting non-bonded forces from GROMACS

Hi, You can make a version of your topology without the bonded interactions, regenerate the tpr and use gmx mdrun -rerun. But there is no force field for which this is known to be useful for any purpose (ie correlate with something physical). Additive force fields are not built to be decomposable

Re: [gmx-users] simulation continuation without -t option

should use -t option. Is it like -t option ensures to use the last position > and coordinates even though one mentions > gen_vel as yes in .mdp file? > > Sincerely, > > Prabir > > On Thu, Sep 19, 2019 at 12:08 PM Mark Abraham > wrote: > > > Hi, > > > >

Re: [gmx-users] simulation continuation without -t option

Hi, If grompp sees that your .mdp file asks for it to generate velocities, it does so and reports it in the terminal output. You will see that for your NVT grompp and not for your NPT grompp. You can also use gmx dump -s the.tpr to observe whether the velocities match the input you gave to the

Re: [gmx-users] RAM usage of gmx msd

Hi, It's likely that using the same index file is the problem. The numbers it contains are interpreted relative to the tpr file, so if you make a subset of the tpr file, then it's on you to understand whether the necessary indices have changed or not. Mark On Tue, 17 Sep 2019 at 14:58, Martin

Re: [gmx-users] What is the equivalent command for insert-molecules in Gromacs 3.3.1?

Hi, The file formats read by grompp haven't changed, so you can prepare your system with a modern version of GROMACS, and call grompp for that old one. But I have a hard time imagining a method that was implemented in 3.3.1 still being useful. Even an enhanced sampling method would have to

Re: [gmx-users] Batch mode error in GROMACS version 2019.2

> > > > > >> Hi Mark, > > >> > > >> Thanks! > > >> > > >> Interactively I could do it without any error. However, this error > only > > >> arises whenever I have tried to use batch mode. > > >> > > >

Re: [gmx-users] Batch mode error in GROMACS version 2019.2

What happens when you do it interactively? Mark On Fri, 13 Sep 2019 at 14:21, Rajib Biswas wrote: > Dear All, > > I am trying to use the post-processing tools in batch mode. I am using the > following commands > > echo 18 0 | gmx_mpi energy -f traj.edr -o temperature > > Getting the following

Re: [gmx-users] Fwd: SIMD options

rce=link_campaign=sig-email_content=webmail > > > Mail > priva di virus. www.avast.com > < > https://www.avast.com/sig-email?utm_medium=email_source=link_campaign=sig-email_content=webmail > > > <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> > > Il giorno gio 12 se

Re: [gmx-users] Fwd: SIMD options

Hi, There will have been reports by cmake about whether the detection program compiled and/or ran successfully, which would be useful diagnostic information. Please run cmake in a fresh build directory and look for that. It is possible to run that program individually, if the issue is that it

Re: [gmx-users] How can Build gromacs using MSVC on Win64 with AVX2?

Hi, Those are kernels for legacy code that never use such simd anywhere Mark On Thu., 12 Sep. 2019, 07:16 Tatsuro MATSUOKA, wrote: > On GROMACS 2019.3, GROMACS cannot be built with AVX2. > > In gmxSimdFlags.cmake > > SIMD_AVX2_C_FLAGS SIMD_AVX2_CXX_FLAGS >

Re: [gmx-users] Fat-bottom restrain

erved En.-2.97263e+06 89 1.81911e+06 6.30101e+06 > >> (kJ/mol) > >> > >> As can be seen above the Flat-bottom posres energy is just zero during > >> the simulation; and even stiffening the force constant from 4184 > KJ/(mo

Re: [gmx-users] Using -multidir option on Cray (aprun)

Hi, Putting the mdrun_mpi command into a variable makes sense, but the rest of the command line makes sense directly, so you get the shell expansions you might intend. Mark On Wed, 11 Sep 2019 at 08:53, Suman Chakrabarty wrote: > Dear all, > > I have managed to resolve this issue, which was a

Re: [gmx-users] grompp not possible with annealing - Gromacs 2019.1

Hi, Thanks for the report - but it's probably fixed already ( http://manual.gromacs.org/documentation/2019.2/release-notes/2019/2019.2.html#fix-segmentation-fault-when-preparing-simulated-annealing-inputs) so I suggest you get the latest 2019.x release? Mark On Tue, 10 Sep 2019 at 17:15,

Re: [gmx-users] MSVC or later now supports AVX2 and AVX_512

Hi, Thanks for the report. Do the tests pass? Particularly the simd-test binary. Mark On Tue, 10 Sep 2019 at 09:36, Tatsuro MATSUOKA wrote: > In gmxSimdFlags.cmake, it is described : > # no AVX2-specific flag for MSVC yet > > However, at least MSVC 2017 and 2019, /arch:AVX2 is added. > If I

Re: [gmx-users] Load imbalancing

Hi, On Mon, 9 Sep 2019 at 12:01, Bratin Kumar Das <177cy500.bra...@nitk.edu.in> wrote: > Dear all, > I am running REMD simulation with 65 replicas. When the > simulation is running , I checked the .log file for every replica. In some > replicas I am getting more than 10% load

Re: [gmx-users] gromacs lincs warning: relative constraint deviation after lincs

ut.gro is pausing the script. > Can this be a possible reason? > > On Sat, 7 Sep 2019 at 20:06, Mark Abraham > wrote: > > > Hi, > > > > Such errors do lead to a normal gmx mdrun aborting. So the question is > more > > what is in your script that might affect

Re: [gmx-users] The problem of utilizing multiple GPU

90 ns/day. However, > when I don't assign the GPU but let all GPU work by: > >gmx mdrun -v -deffnm md > > The simulation performance is only 2 ns/day. > >> So what is correct command to make a full use of all GPUs and achieve > the best performance (which I expect should be much higher than 90 ns/day &g

Re: [gmx-users] Fat-bottom restrain

Hi, The total potential energy violating the restraints is reported, so you should see that there is an appropriate contribution there, and probably plan to stiffen the force constant. Mark On Fri., 6 Sep. 2019, 17:23 Alex, wrote: > Dear all, > Using the flat-bottom (K=4184 KJ/(mol. nm^2))

Re: [gmx-users] pressure is coming 1.39

Hi, Without a statistical error estimation and a target pressure, the question can't be answered. Pressure takes time to measure, and you need to do so only after equilibration. 1.39 +/- 3 bar might be fine Mark On Sat., 7 Sep. 2019, 07:48 Bratin Kumar Das, <177cy500.bra...@nitk.edu.in> wrote:

Re: [gmx-users] gromacs lincs warning: relative constraint deviation after lincs

Hi, Such errors do lead to a normal gmx mdrun aborting. So the question is more what is in your script that might affect that? Mark On Sat., 7 Sep. 2019, 07:39 rajat punia, wrote: > Hi, I am trying to run multiple (1000) md simulations using a shell script. > Some of the simulations (say

Re: [gmx-users] The problem of utilizing multiple GPU

Hi, On Wed, 4 Sep 2019 at 12:54, sunyeping wrote: > Dear everyone, > > I am trying to do simulation with a workstation with 72 core and 8 geforce > 1080 GPUs. > 72 cores, or just 36 cores each with two hyperthreads? (it matters because you might not want to share cores between simulations,

Re: [gmx-users] REMD-error

Hi, On Wed, 4 Sep 2019 at 10:47, Bratin Kumar Das <177cy500.bra...@nitk.edu.in> wrote: > Respected Mark Abraham, > The command-line and the job > submission script is given below > > #!/bin/bash > #SBATCH -n 130 # Number

Re: [gmx-users] REMD-error

Hi, We need to see your command line in order to have a chance of helping. Mark On Wed, 4 Sep 2019 at 05:46, Bratin Kumar Das <177cy500.bra...@nitk.edu.in> wrote: > Dear all, > I am running one REMD simulation with 65 replicas. I am using > 130 cores for the simulation. I am

Re: [gmx-users] MDrun Slow!

Hi, Please do check out the install guide for advice on how to build for the hardware you plan to run on. The defaults will just do the right thing for you :-) Mark On Thu, 29 Aug 2019 at 14:26, Quin K wrote: > Hi > When I do a mdrun it gives me a message saying, > > Compiled SIMD: SSE2, but

Re: [gmx-users] energy minimization

Hi, Typical force fields will have negative energies at minimize configurations, but my guess is that your initial configuration has some serious problem. Did you visualise the minimization start and end points? Mark On Tue., 27 Aug. 2019, 18:52 Dhrubajyoti Maji, wrote: > Dear gromacs users,

Re: [gmx-users] HtoD cudaMemcpyAsync failed: invalid argument

led: invalid argument) > > . Its running on CPU, but not on GPU. Work of 3 days will take 15 days. > Already completed simulation for other complexes. This complex creating > problem due to vsites3. PLEASE HELP DEADLINE IS APPROACHING. > > On Tue, Aug 27, 2019 at 12:23 AM M

Re: [gmx-users] Performance, gpu

og -v -dlb yes > -gcom 1 -nb gpu -npme 44 -ntomp 4 -ntomp_pme 6 -tunepme yes > > would you please help me choose a correct combinations of -npme and ... > to get a better performance, according to the attached case.log file in my > previous email? > Regards, > Alex > &

Re: [gmx-users] Still "GB parameter(s) missing or negative for atom type 'C'" issue after 7 years

Hi, The answer is still the same - if gbsa.itp has the right contents, is it being included at the right time? Mark On Wed, 28 Aug 2019 at 12:57, Vedat Durmaz wrote: > Sorry, typo: "I can NOT get my system grompped" ... > > > Am 28.08.19 um 12:03 schrieb Vedat Durmaz: > > Hi everybody, > > >

Re: [gmx-users] Index file

Hi, There's lots of documentation and examples available. See http://manual.gromacs.org/documentation/current/user-guide/cmdline.html#selection-syntax-and-usage Mark On Wed, 28 Aug 2019 at 07:14, Omkar Singh wrote: > Hi everyone > Can anyone help me regarding "gmx select" command making a

Re: [gmx-users] HtoD cudaMemcpyAsync failed: invalid argument

e atom numbers."as I was using 2018.4. So I switched to > version-16. But now trapped in this HtoD cudaMemcpyAsync failed: invalid > argumenterror. > > On Tue, Aug 27, 2019 at 12:09 AM Mark Abraham > wrote: > > > Hi, > > > > You're running 2016.x which ha

Re: [gmx-users] HtoD cudaMemcpyAsync failed: invalid argument

eter Tieleman > Teemu Virolainen Christian WennbergMaarten Wolf > and the project leaders: > Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel > > Copyright (c) 1991-2000, University of Groningen, The Netherlands. > Copyright (c) 20

Re: [gmx-users] CHOL still not recognised

Hi, You should follow the error message instructions "... they should not have the same chain ID as the adjacent protein chain" which you know is that X. Make the protein have a different chain ID from the rest. Mark On Mon, 26 Aug 2019 at 19:27, Ayesha Fatima wrote: > Dear Justin, > Thank

Re: [gmx-users] Gromacs 2019.3 compilation with GPU support

Hi, All versions of icc requires a standard library from an installation of gcc. There are various dependencies between them, and your system admins should have an idea which one is known to work well in your case. If you need to help the GROMACS build find the right one, do check out the GROMACS

Re: [gmx-users] Topology

Hi, You already have the topology for it :-) Chirality is about spatial configuration, topologies are about connectivity. There's no need to try to encode the spatial configuration because there is no accessible path for the conversion, given the existence of the bonded parameters.

Re: [gmx-users] Switching CPU to GPU in a simulation

Hi, As mdrun has the "feature" that when short-range nonbonded are on the GPU, any energygroups have zero values output each step, you can continue happily, but of course you won't have a useful analysis. If you need those energy groups, then you'll need to plan to do a rerun (and then recent

Re: [gmx-users] Performance, gpu

Hi, There's a thread oversubscription warning in your log file that you should definitely have read and acted upon :-) I'd be running more like one PP rank per gpu and 4 PME ranks, picking ntomp and ntomp_pme according to what gives best performance (which could require configuring your MPI

Re: [gmx-users] typedefs.h in gromacs installation

Hi, You can use only GROMACS versions that gromos++ supports. Hopefully they've documented which ones those are :-) Mark On Tue, 20 Aug 2019 at 15:47, Johannes Hermann wrote: > Hi Justin, > > Thanks! So this is a gromos++ problem? The gromos++ developers should > update the linking during

Re: [gmx-users] WARNING

Hi, You're doing a rerun from a trajectory file that probably doesn't have velocities in it. mdrun can compute potential energies from the position coordinates, but these other quantities can't be computed from just the position coordinates. mdrun can't know what you're expecting to be correct,

Re: [gmx-users] Gromacs FEP tutorial

Hi, To which tutorial are you referring? Mark On Mon., 19 Aug. 2019, 19:09 Alex Mathew, wrote: > Can anyone tell me which thermodynamics cycle was used in the tutorial? for > FEP. > -- > Gromacs Users mailing list > > * Please search the archive at >

Re: [gmx-users] Running on two nodes

Hi, There's lots of this kind of information reported in the log file, including the number of nodes that the MPI environment has made available to mdrun. Mark On Sat, 10 Aug 2019 at 14:15, Searle Duay wrote: > Hello! > > I am trying to run a simulation on two nodes. Each node has 2 GPUs and

Re: [gmx-users] Relation between tau_t and nstxout

Hi, On Thu, 8 Aug 2019 at 18:41, Neena Susan Eappen < neena.susaneap...@mail.utoronto.ca> wrote: > Hello gromacs users, > > I am using Nose-hoover thermostat, is it correct to say that tau_t has to > be less than or equal to nstxout/ nstvout? No. tau_t describes the rigidity of the coupling.

Re: [gmx-users] Gromacs 4.5.7 compatibility with Titan X GPU

Hi, Unfortunately that version of GROMACS hasn't been tested or supported in well over five years, so probably it is simply incompatible with modern GPUs. You could try explicit solvent in modern GROMACS, which might be comparably fast with that old version :-) Or AMBER if you really need

Re: [gmx-users] inputfile character related issue

Hi, We don't have any useful information to go on, but I'll guess that you've edited the file e.g. on Windows using a not-very-suitable editor and the line endings are no longer recognizable elsewhere. Try converting the file, e.g. with the dos2unix utility. Mark On Mon, 5 Aug 2019 at 16:13,

Re: [gmx-users] best performance on GPU

Hi, We can't tell whether or what the problem is without more information. Please upload your .log file to a file sharing service and post a link. Mark On Fri, 2 Aug 2019 at 01:05, Maryam wrote: > Dear all > I want to run a simulation of approximately 12000 atoms system in gromacs > 2016.6 on

Re: [gmx-users] mdrun: In option s, required option was not provided and the default file 'topol' does not exist or not accessible and non-integer charges

Hi, What does ls -l return when run from your working directory? Mark On Fri, 2 Aug 2019 at 01:49, Mohammed I Sorour wrote: > Hello Dr. Dallas, > > Yes, the nvt.tpr was created and I had it in the local directory ready for > the mdrun. > Yes, those copy/pastes of the commands I used. > Since

Re: [gmx-users] performance issues running gromacs with more than 1 gpu card in slurm

Justin > > > —— > > Carlos Navarro Retamal > > Bioinformatic Engineering. PhD. > > Postdoctoral Researcher in Center of Bioinformatics and Molecular > > Simulations > > Universidad de Talca > > Av. Lircay S/N, Talca, Chile > > E: carlos.navarr

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