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Questions related to Gromacs
After 5 minutes of Chemiluminescence substrate incubation, the image was reversed. Any ideas on how to make it better?
16 June 2025 5,357 0 View
I'm doing a Western blot and haven't seen any protein for two months. After transferring, the marker is visible, but when I detect the protein once, wash it, and try to detect another protein the...
22 May 2025 583 3 View
I want to run a classical molecular dynamics simulation of Ti4+ in aqueous solution. However, I am unable to find the sigma and epsilon parameters for Ti4+ from literature.
12 December 2024 7,187 1 View
I have a 2D nanostructured drug complex. I want to run an MD simulation for the same using GROMACS. I could not create the force field as it shows errors every time. Can anyone help me?
26 November 2024 5,896 4 View
Hello everyone, I am calculating the duration from Site Selection to Clinical Start Date for the process map. The duration across all groups ranges from 0 to 70 months, with mean of 5.6 months...
04 May 2024 2,676 4 View
In Materials Studio, I can't select an atom or atoms by clicking and dragging. I can select only bonds in 3D model by clicking or dragging. What's the problem?
31 January 2024 1,320 1 View
I am trying to do a single-point polarizability calculation with TDDFT with input : #p polar td=(nstates=8) M062X/6-31+g(d,p) geom=connectivity I am getting an error like: The selected state is...
17 January 2024 9,396 4 View
I have a protein structure loaded into VMD, it has multiple chains. I would like to get the number of chains, and the number of amino acids in each chain using a Tcl script. Does anyone know how...
16 January 2024 7,770 2 View
I just doing an experiment in my lab for copolymerization Acrylic acid and maleic acid using hydrogen peroxide as initiator in 103 degC. But, why in my Polymerization process forming a foam?
15 January 2024 2,185 7 View
I would like to have GPU support for GROMACS, my GPU is Intel Iris Xe Graphics, so I was recommended to use SYCL support. So I would like to ask if anyone knows how to proceed to install...
18 December 2023 9,271 5 View
I'm looking to calculate charges for my ligand and later run MD simulation on them. I ran into this error suddenly when it had worked in the past. I have Gaussian 16 installed. My slurm.out Net...
01 December 2023 5,168 1 View
The graph below is a plot of RDF from Gromacs MD. It was reported that the coordination number of one substance round another (for here CO2 round anion) can be obtained from the relation: CN = 4 x...
18 November 2023 8,930 0 View
Can anyone help me parametrize Si atoms in gromacs forcefields. how can i include parameters in ffnonbonded and bonded and atomtype files of gromacs forcefield for example oplsaa or charmm? (I...
12 November 2023 8,659 3 View
dear All when i gave densmap command in gromacs gmx densmap -f MD_center_noPBC.xtc -s MD.tpr -n index.ndx -aver z -bin 0.05 -dmin 0 I got a very big density.xpm file. Please suggest how to...
30 September 2023 239 0 View
I have received the data from RT-qPCR and I want to start a statistical analysis. The first step is the normality check. I have 2 diferrent plant tissues (close related,same family), one gene of...
27 September 2023 8,279 1 View
I predicted a protein structure using trRosetta. I couldn't do homology modeling as no homologs are present. the model contains tryptophan but the indol group of tryptophan lacks one carbon. (...
26 September 2023 10,022 1 View
What are the most important accredited programs in drug design?
24 September 2023 6,390 0 View
I am working on predicting the 3D structure of a protein with an amino acid sequence exceeding 3000 residues. Unfortunately, the full structure for this protein is not available in the Protein...
20 September 2023 3,916 2 View
In the a molecule I am working on, there is a certain O-H bond. I wanted to study the variation of energy on changing the bond length, for that I did a relax-scan computation on g16. I have...
09 September 2023 3,843 3 View
The Fattal error is The atomtype CAro not found, I am using 54a7 force field in gromacs 2021.4 version, since I work in clusters, I don't have its acces to upgrade the force field files, please...
04 September 2023 8,650 2 View
I am currently learning a new data analysis program and have found RStudio to be a user-friendly and efficient software. As I work, I am curious if there is a package or code available that can...
10 August 2023 2,171 3 View
I was working on a gene construct synthesized in pet29 vector as a clone. Primers were prepared and optimized with gene at Tm 58 degrees. Once primers were optimized, I carried out transformation...
09 August 2023 8,231 4 View
hi I wanted to draw diagram" the relative shape asymmetry parameter for inclusion of ligand into the b-CD cavity" with gromacs. I kindly beseech your counsel and guidance in navigating this endeavor.
08 August 2023 5,333 1 View
I have lipid bilayer which is pack in packmol, after solvation in GROMACS, I don't want the water molecule in the lipid tail region for MD simulation. So can anyone help me to remove the water...
28 July 2023 1,300 12 View