How to resolve "make check" tests errors in gromacs installation?

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Is there any way to count the number of water molecules around a ligand during simulation of its binding pathway?

I would like to calculate the presence of water molecules number as a function of time, around a ligand during binding to its pocket from a trj.xtc file. How can I do it by Gromacs or any other...

10 November 2018 9,189 10 View

Getting an fatal error when rerunning .trr trajectory in Gromacs?

Dear Gromacs Users When I rerun .trr trajectory files for re-calculating energies and forces, the following error was received. Any suggestion to solve it please? However, there is no problem with...

06 July 2018 9,746 1 View

How to calculate the oxidation number of Fe atom and the multiplicity of a Fe2S2 cluster?

I want to calculate Fe2S2 charges in a protein complex, but I don't know how to obtain the multiplicity, suitable oxidation number of Fe in Fe2S2 cluster, Is it oxidation state +3 for Fe? Which...

11 December 2016 6,235 4 View

Is there a program to create topology files (.rtp, .itp, .hdp .atp and .dat) for various force fields in gromacs from a New Residue PDB file?

Dear Researchers I have already used from gromacs manual for editing topology files (http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field), but I am looking for program...

08 September 2016 427 9 View

How can I make a movie from gromacs trajectory file (200 ns)?

VMD failed because of low memory of computer (16GB) for resolving this problem, Can I split .xtc files to two parts? How?

10 November 2015 6,235 8 View

How to analyze a particular region of my simulation box in GROMACS?

Hi, I am using GROMACS 5.1.4 to simulate water in contact with a surface. I am only interested to calculate some properties of water near the surface. Let's say at a distance of x nm from the...

03 March 2021 9,989 2 View

What's the best way to measure growth rates in House sparrow chicks from day 2 to day 10?

What's the best way to measure growth rates in House sparrow chicks from day 2 to day 10? Since, the growth curve from day 2 to 10 won't be like the "Logistic curve" it might not follow logistic...

03 March 2021 1,401 3 View

After a reference from Int J Body Compos Res, can any body help?

Hi, I am after the reference below, my library says it cannot obtain a copy either locally or internationally, any help appreciated! Chris Wang ZM, Heshka S, Wielopolski L, Pi-Sunyer FX, Pierson...

03 March 2021 6,193 1 View

What techniques can I use to determine the miscibility of polymer blends?

The term miscibility refers to the single-phase state in thermodynamics. I do not mean the compatibility of different components. To determine the miscibility I know several techniques such as...

03 March 2021 4,107 4 View

How to repeat an operation on an atom selection for multiple times in PyMol?

Hi, I am trying to construct a multi-layer fibril structure from a single layer in PyMol by translating the layer along the fibril axis. For now, I am able to use the Translate command in PyMol...

02 March 2021 4,569 4 View

Shall I skip the measurement model in SmartPLS?

Hello everyone, I had run a mediation model in SmartPLS using questionnaires that were already validated among my statistical population. A professor who edited my paper -though she is not...

01 March 2021 3,052 3 View

What is involved in morphological changes of SEM images of a substance?

In the sem analysis of CaCO3 nanaoparticles, the morphology images showed spherical shaped particles but the proposed morphology for these type of nanoparticles is trigonal. I prepared the...

01 March 2021 1,960 4 View

Joint behaviour in Abaqus is not captured well?

I am working on roof joint and trying to simulate the behaviour in Abaqus. I am successful in running the model but the final graph does not follow the experimental curve in the negative direction...

01 March 2021 6,661 3 View

Why might my GFP tag be dissociating from my plasmid after transfection?

I have a set of stably transfected cell lines all transfected with plasmids containing GFP tags on the C terminus. During a western blot using anti-GFP antibody, one of my plasmids has dissociated...

01 March 2021 9,310 4 View

Precipitate after adding laemmli buffer to protein solution containing Potassium Acetate?

Hi, I am running a size exclusion chromatography experiment with a buffer containing Potassium Acetate as a salt. I analyse these fractions through SDS-PAGE. After boiling my SEC fractions in...

01 March 2021 2,622 3 View

Martin Klvana

There is one additional error message in "errors.txt" that precedes the two error messages you have mentioned:

"Fatal error:

Environment variable OMP_NUM_THREADS (4) and the number of threads requested on the command line (1) have different values. Either omit one, or set them both to the same value."

Hassan Aryapour

I used the following command to define number of threads, but had not effect on the results.

set OMP_NUM_THREADS=8

How to solve this problem?