[gmx-users] energy minimization

Hi; I've alreadyconverted the amber topology and coordinate files to gromacs format.But when I want to start running theenergy minimization first by using the grompp to generate .tpr file,I get this error: Program gmx, VERSION5.0.2Source code

Re: [gmx-users] mdrun writes gro file in two different formats and failed visualization of trajectories

On 8/19/15 7:22 AM, anu chandra wrote: Dear Gromacs users, I just noticed that during simulation 'mdrun' writes gro file in two formats - one with broken molecules at the boundaries and other one where surface molecules are perfectly wrapped. Interestingly, this difference in format depends

Re: [gmx-users] Error while configuring gmx-3.3.1

1. I am using it with CPMD as they have mentioned this version of gromacs only. 2. The top-level force fields are not included as they are not present in /usr/local/gromacs/share/top/ file for eg. BH4_oplsaa.itp, however its there in the gmx-3.3.1_qmmm-1.3.2/share/top folder. 3. There is no

[gmx-users] Problem compiling Gromacs 5.1

Hi, I am unable to compile Gromamcs 5.1 using the following cmake command. cmake .. -DGMX_FFT_LIBRARY=fftpack -DCMAKE_INSTALL_PREFIX=gromacs/gromacs-5.1 -DGMX_DOUBLE=off -DGMX_THREAD_MPI=off -DGMX_MPI=on -DGMX_CPU_ACCELERATION=SSE4.1 -DGMX_USE_RDTSCP=off Then I got the error message. Boost =

Re: [gmx-users] Problem compiling Gromacs 5.1

Hi, As the error says you should get a version =1.44 for the boost libraries On 19/08/15 15:49, 岡部篤俊 wrote: g minimal internal version. T -- Felipe Merino Max Planck Institute for Molecular Physiology Department of Structural Biochemistry Otto-Hahn-Str. 11 44227 Dortmund Phone: +49 231 133

Re: [gmx-users] Cl topology in gromacs

Sounds like a question for the acpype developers directly :-) Mark On Wed, Aug 19, 2015 at 8:52 AM Albert mailmd2...@gmail.com wrote: Hello: I am using acpype to create ligand topology. However, I noticed that acpype may not recogonize Cl element which is a halogen atom correctly. After

Re: [gmx-users] Problem compiling Gromacs 5.1

Hi, On Wed, Aug 19, 2015 at 3:49 PM 岡部篤俊 atsutoshi0...@gmail.com wrote: Hi, I am unable to compile Gromamcs 5.1 using the following cmake command. cmake .. -DGMX_FFT_LIBRARY=fftpack -DCMAKE_INSTALL_PREFIX=gromacs/gromacs-5.1 -DGMX_DOUBLE=off -DGMX_THREAD_MPI=off -DGMX_MPI=on

[gmx-users] energy minimization

Hi; I've alreadyconverted the amber topology and coordinate files to gromacs format.But when I want to start running theenergy minimization first by using the grompp to generate .tpr file,I get this error: Program gmx, VERSION5.0.2Source code

Re: [gmx-users] Error while configuring gmx-3.3.1

Hi, Please use a more recent GROMACS version, unless you are actually a forensic archaeologist. Mark On Wed, Aug 19, 2015 at 1:58 PM Padmani Sandhu padmanisandh...@gmail.com wrote: Hello everyone, I am trying to install gmx-3.3.1 on ubuntu 14.04. I have compiled it using following

Re: [gmx-users] Error while configuring gmx-3.3.1

On 8/19/15 7:58 AM, Padmani Sandhu wrote: Hello everyone, I am trying to install gmx-3.3.1 on ubuntu 14.04. I have compiled it using following commands: Any reason you're using wildly outdated software? ./configure make sudo make install *However the program was installed but while

Re: [gmx-users] conformational entropy with/without jumps

Hi Ahmet, Have you looked at the trajectories? Is the molecule really whole/centered? Cheers, Tsjerk T On Wed, Aug 19, 2015 at 3:32 PM, Ahmet Yıldırım ahmedo...@gmail.com wrote: Dear users, I am trying to get the conformational entropy of some structures but the results I got are

[gmx-users] Error while configuring gmx-3.3.1

Hello everyone, I am trying to install gmx-3.3.1 on ubuntu 14.04. I have compiled it using following commands: ./configure make sudo make install *However the program was installed but while running grommp, it was terminated with an error :* checking input for internal consistency... calling

[gmx-users] mdrun writes gro file in two different formats and failed visualization of trajectories

Dear Gromacs users, I just noticed that during simulation 'mdrun' writes gro file in two formats - one with broken molecules at the boundaries and other one where surface molecules are perfectly wrapped. Interestingly, this difference in format depends on where I run the simulation - either in a

Re: [gmx-users] Thread, Multiple gpu, and sharing node

Hi, CPUs and GPUs are not created equal, so there's not enough information to say anything. But 3k atoms will not keep most GPUs fully busy, so you will want to consider running multiple replicates of your system, e.g. with mdrun -multi. See also http://arxiv.org/abs/1507.00898 Mark On Tue, Aug

[gmx-users] conformational entropy with/without jumps

Dear users, I am trying to get the conformational entropy of some structures but the results I got are strange. I tried two methods. I removed jumps from trajectory and centered the protein in box (1). I used the raw trajectory (2). GROMACS gives different results for each processes. Which

Re: [gmx-users] Tesla K40 and K80 performance for Gromacs

Hi, Yes, one chip on the dual chip K80 GPU (as long as it's cooled well) will be roughly as fast as a K40 with GROMACS. Otherwise, the setup looks well-balanced, it should give good performance with GROMACS! Note that you can save money on: - SSD which is not necessary for GROMACS production

Re: [gmx-users] Problem compiling Gromacs 5.1

Yeah sorry, I realized later that I did not read the complete thing... Bad habit. On 19/08/15 16:18, Mark Abraham wrote: Hi, No, the warning about Boost versions is unrelated and just happens to precede the issue. Mark On Wed, Aug 19, 2015 at 4:13 PM Felipe Merino

Re: [gmx-users] reproducibility of trajectory

Thank you, Mark. Got it. Qing At 2015-08-19 17:32:22, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, You've observed a single event. By itself that doesn't mean much of anything. If you were in a car crash today, that doesn't mean you will be in one every time you go on the road. But if you

[gmx-users] distance issues with umbrella sampling

As far as I¹ve understood, the absolute distance reported using g_dist (note: alternative name in 5+) and the reported harmonic potential between two groups using pull code in grompp, doesn¹t always match. As such, I some times end up with neighbouring umbrella histograms practically sitting on

Re: [gmx-users] distance issues with umbrella sampling

Nash, Anthony a.nash@... writes: As far as I¹ve understood, the absolute distance reported using g_dist (note: alternative name in 5+) and the reported harmonic potential between two groups using pull code in grompp, doesn¹t always match. As such, I some times end up with neighbouring

[gmx-users] AIX XLC Gromacs-5.1-rc1. Undefined reference. Underscore issue.

Helo guys! I'm trying to compile Gromacs-5.1-rc1 with XLC 13.1.2 ESSL 5.3 and I'm facing an undefined reference error. Here's what I got: $ cd /home/ibm/crash/gromacs-agosto/2/gromacs-5.1-rc1/single/share/template /usr/bin/cmake -E cmake_link_script CMakeFiles/template.dir/link.txt --verbose=1

[gmx-users] trjconv -dt issue

Hello, I have a quite long continuous trajectory coming from several initial input pieces (cluster crashed...) that I want to downsample, as a start from 0.5ps timestep in the source files to just 1ps and later bigger timesteps. Using the -dt option of trjconv (GROMACS 4.6.5.), there seem to be

Re: [gmx-users] Problem compiling Gromacs 5.1

Line 52 of cmake/FindSphinx.cmake file is written below. string(REGEX REPLACE Sphinx \\([^)]*\\) ([^ ]+) \\1 SPHINX_EXECUTABLE_VERSION ${SPHINX_VERSION_OUTPUT_VARIABLE}) Can you tell me how I can change the line? Bests, Leucer 2015/08/19 23:11、Mark Abraham mark.j.abra...@gmail.com のメッセージ:

[gmx-users] energy minimization

Hi; I've alreadyconverted the amber topology and coordinate files to gromacs format.But when I want to start running theenergy minimization first by using the grompp to generate .tpr file,I get this error: Program gmx, VERSION5.0.2Source code

[gmx-users] energy minimization

Hi;I've alreadyconverted the amber topology and coordinate files to gromacs format.But when I want to start running theenergy minimization first by using the grompp to generate .tpr file,I get this error: Program gmx, VERSION5.0.2Source code

[gmx-users] Cl topology in gromacs

Hello: I am using acpype to create ligand topology. However, I noticed that acpype may not recogonize Cl element which is a halogen atom correctly. After acpype, it generate a new ligand pdb file called: lig_NEW.pdb and I found the following: ATOM 10 C09 UNK Z 1 11.502 -10.939

Re: [gmx-users] reproducibility of trajectory

Hi, You've observed a single event. By itself that doesn't mean much of anything. If you were in a car crash today, that doesn't mean you will be in one every time you go on the road. But if you observe yourself in a car crash every day, now you have evidence that you need driving lessons... If

Re: [gmx-users] Few queries about microsecond long simulations

Hi Anu, Since .xtc doesn't store velocities, its a much more compact trajectory than it's .trr counterpart, i.e. it has a smaller size. Also, .xtc is more easier on your computer RAM than the .trr file, during visualizing or analyzing using the .xtc trajectories. If you are looking to save disk

Re: [gmx-users] Few queries about microsecond long simulations

Hi Anu, Again that is up to you. I do not save a full precision file for my analysis. In the infinite disk space (and time!) limit of course you would like to have veolcities, forces, and positions of all atoms very frequently. However, if you do not foresee any analysis requiring velocities

[gmx-users] reproducibility of trajectory

Hi, I did a 200-ns MD for a protein and found an interesting conformation transition, and according to NMR study in literature, it is believed that 10 us ~ ms scale simulations are needed to get this conformation transition. However, when I tried to reproduce this conformation transition, I was

Re: [gmx-users] Error while configuring gmx-3.3.1

Hello Justin, I have copied both the .itp files which were giving error in to /usr/local/gromacs/share/top using command: sudo cp BH4_oplsaa.itp /usr/local/gromacs/share/top sudo cp ffoplsaabon.itp /usr/local/gromacs/share/top and now grompp worked. Please can you suggest me any solution so