Solving gromacs problem

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I am working on my Master's thesis on the biogeography of the genus Ruagea and I would like to ask, could someone help me to check whether my result?

I created a file with my outgroup and ingroup species using Beauti, ran it in BEAST, viewed it in Tracer, and then used TreeAnnotator to create a file that I imported into RASP. Could someone...

28 July 2024 2,979 1 View

Can telekinesis, telepathy, and prediction be achieved through science?

Information in The Three Dimensions of Time.Information in The Three Dimensions of Time Information Transfer based on Brains Entanglement.Information Transfer based on Brains Entanglement Time...

28 July 2024 7,522 0 View

Is it possible that the Earth's axis of rotation could change?

Due to the shifting ocean currents, the planet could be thrown off balance, altering the angle of rotation, and even causing the axis to shift, plunging us into chaos. In reality, it doesn't take...

15 July 2024 8,949 1 View

Can we calculate the CO2 adsorption capacity(mmol/g) of a solid adsorbent (MOF) using CO2_TPD analysis?

what is the relationship b/w TCD signal(a.u) and CO2 desorbed (mmol/g) ? can we plot CO2 desorbed(mmol/g) Vs Time(min) from TPD data?

15 July 2024 3,248 1 View

How can I regenerate a SCX column modified with Sulfonate group (Thermo 054995)? The colmun has lost its Resolution and peak to valley ratio?

The column is used in Ion Exchange Chromatography of Monoclonal antibodies and the method of analysis is based on pH gradint.

13 July 2024 7,462 1 View

Does sucrose interfere with the BCA reagent in peptide concentration assays?

Hello everyone! I am currently working on the expression and purification of an antimicrobial peptide that experiences reduced activity after each freeze-thaw cycle. To improve its stability, I...

10 July 2024 6,830 1 View

What is the reason of stacking DNA in agarose gel well?

we electrophoresis PCR product on 0.7% agarose gel at 120V for 1 hour, our target size is 5000 bp but our DNA stack at wells and do not com in to gelldo you have any suggestion for this?

02 July 2024 5,235 0 View

Is it possible to increase the intensity of UV-vis absorption of DNA EITH A LIGAND IN the groove BINDING mode?

Is it possible to increase the intensity of UV-vis absorption in the interaction of the groove connection mode?

29 June 2024 4,867 4 View

Hello, I wanted to know if it is a necessity to perform MTT test in three time points to evaluate the cytotoxicity of a metal alloy?

I am working on a magnesium based alloy, and i wanted to evaluate the cytotoxicity of my alloy with MTT assay. I want to know the reason why most of the researchers perform the MTT assay in three...

28 June 2024 2,570 1 View

Population coverage analysis for some MHC II alleles?

Hello everyone Does anyone know how could we determine population coverage of some MHC II alleles such as HLA-DRB3*02:02, HLA-DRB5*0101, HLA-DPA1*02:01-DPB1*05:01, HLA-DRB4*01:01,...

20 June 2024 2,155 1 View

Gromacs first step of minimization ?

I have face this problem anyone help me how to solve this issue ?which is below Fatal error: There are inconsistent shifts over periodic boundaries in a molecule type consisting of 78 atoms. The...

07 August 2024 2,598 1 View

How to restart MD without using checkpint file in GROMACS?

Dear All Gromacs User I would like to restart MD without using checkpint .cpt files? I heard there is a way for acheiveing this. Any input and sugegstions are most welcome. Thanking You Budheswar

29 July 2024 3,084 8 View

How to prepare a molecule for molecular dynamics calculations?

If I want to calculate molecular dynamics (Gromacs), do I first need to optimize the geometry of the molecule? For example, I first draw the molecule in Avogadro, and then what? I guess I can't...

28 July 2024 673 3 View

Wrong out put for gmx x2top?

Dear users, I would like to simulate a zeolite structure in gromacs. I got the .cif file from IZA expanded in one direction in Materials Studio and exported a .pdb file. However, when I want to...

24 July 2024 367 4 View

Why binding energy is in positive number after performing mmpbsa?

I performed mmpbsa of protein-protein complex simulation on gromacs. My binding free energy is +166781. This complex is stable when experimentally produced in wet lab. In index.ndx I grouped...

19 July 2024 4,120 5 View

How to resolve ‘[ atomtypes ] Invalid order for directive atomtypes’ error in Gromacs?

I have been using Gromacs 2021.7. I wanted to simulate two small molecules in water. But, while generating the ions.tpr, I am getting the following error. The topol.top and .itp files for each...

17 July 2024 9,897 4 View

Getting this error : gmx_mpi': corrupted size vs. prev_size: 0x0000000001d1b320 ***?

i am using the trjconv command in gromacs gmx_mpi -debug trjconv -s md.gro -f md.xtc -o utr.xtc -fit rot+trans and after few steps i got the error gmx_mpi': corrupted size vs. prev_size:...

17 July 2024 6,216 1 View

Can we find the Gromacs version from XTC file or TRR?

Hello everyone, This soudns like a strange question, but I created five XTC files using five different versions of GROMACS some years ago. All other files are missing, and I want to repeat the...

16 July 2024 7,205 2 View

How to define a zeolite structure with rigid framwork?

Dear Gromacs users, I would like to simulate a zeolite-water system. In different literature, it is suggested to consider a rigid framework of zeolite to decrease the computational cost. I would...

15 July 2024 4,590 1 View

In silico techniques for identification of inhibitor/activator/substrate activity?

Hello dear researchers, I would like to know about available in silico tests that could predict the activity of ligands (small molecules) against the target protein. I have performed docking...

08 July 2024 4,724 4 View