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Questions related to Gromacs
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 2,663 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 1,306 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 9,387 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 7,761 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 2,174 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 9,260 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 5,157 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 8,924 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 8,648 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 228 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 8,269 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 10,011 1 View
What are the most important accredited programs in drug design?
24 September 2023 6,379 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 3,901 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 3,828 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 8,641 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 2,153 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 8,213 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 5,322 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 1,291 12 View
older adukts reason for admisson
07 July 2023 9,932 1 View
The cochlea is small. So I want to know how to get enough and pure RNA.
27 June 2023 2,550 2 View
What is the best DFT functional and basis set for structure optimization of Organic molecules complexes with metals such Cu, Pb, Zn?
12 June 2023 7,719 7 View
Hello What is the the concept of MAT-PROP-NORMALIZED in topology optimization in abaqus? What is the variable?
10 June 2023 6,915 0 View