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Questions related to Gromacs
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 1,205 12 View
older adukts reason for admisson
07 July 2023 9,846 1 View
The cochlea is small. So I want to know how to get enough and pure RNA.
27 June 2023 2,479 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 7,637 7 View
Hello What is the the concept of MAT-PROP-NORMALIZED in topology optimization in abaqus? What is the variable?
10 June 2023 6,832 0 View
Dear Researchers, I am doing molecular Dynamic simulation using GROMACS software. Currently i am working on the sugar modified double stranded DNA, for which i need to generate a force...
07 June 2023 3,894 2 View
I am planning to run GaMD simulation in amber, and I want to produce multiple trajectories of the same system to run independent simulations of the system with different initial velocities. The...
30 May 2023 7,403 1 View
My complex was converged for Maximum force and RMS force at the 45th step when using the SDD basis set, and then remove from convergence after 20 steps. Now, 183 steps have been completed but the...
10 May 2023 2,872 2 View
When i run the command to calculate the H-bonds ''gmx hbond -s md.tpr -f md_center.xtc -num hb.xvg'' I can't find anything ( the file hb.xvg does not contain the number of H-bonds). I also...
06 May 2023 3,413 8 View
How to measure concentration (g of polymer/ g of mixture) of a polymer from mixture of polymers and ceramic materials? I have no background in polymer, hence I am not sure whether (mol of...
05 May 2023 8,299 4 View
I am running the pdb2gmx command for my protein using Gromos 54a7 force field, but I have this error: Fatal error: Atom type OUrea (residue UREA) not found in atomtype database while this atom...
05 May 2023 122 2 View
When generating C code from ST code, MatIEC compiler creates a file with variables for debugging.
23 April 2023 9,166 0 View
I need to calculate the crystallinity of a compound by DSC
13 April 2023 1,732 3 View
As an experimental condition, I am constructing an in-silico lipid bilayer model. I need to know how to calculate their leaflet ratios given the parameter by which the upper-to-lower leaflet ratio...
13 April 2023 5,525 0 View
Hi, An energy minimization step I converged to machine precision with the following values: Potential Energy = -5.0373220e+06 Maximum force = 1.1988365e+03 on atom 6641 Norm of force =...
09 April 2023 2,989 2 View
How can I use amber forcefield in materials studio?
07 April 2023 2,443 0 View
I want to perform MD simulation on a protein that contains water molecules in PDB what forcefield parameters (topology/ parameter ) files should one use ?
27 March 2023 5,761 5 View
Dear Amber user, I want to study the interactions between protein and ions. I am running a simulation with protein, ions and water and I want to save the trajectories of protein and ions. I know...
27 March 2023 5,768 2 View
I want to simulate RNA molecules containing modifications such as PSU with amber ff and GROMACS software. I have the gromacs compatible amber14sb_OL21.ff from https://fch.upol.cz/ff_ol/gmxOL21.php...
16 March 2023 5,893 1 View
I am running final md simulation for 100ns , after 7ns run , showing too many lincs warning , Here is my md.mdp file. title = OPLS Lysozyme NPT equilibration ; Run...
08 March 2023 8,393 2 View
I am running a protein ligand complex simulation using Gromacs 2021 on a Windows Subsystem for Linux. My laptop has Nvidia GeForce RTX 3050 GPU. When i run the simulation of Lysozyme tutorial (as...
07 March 2023 4,721 4 View
Using 1 MPI thread Using 8 OpenMP threads WARNING: Using the slow plain C kernels. This should not happen during routine usage on supported platforms. Back Off! I just backed up em.trr to...
28 February 2023 1,680 1 View
Hello colleagues! I found that my structure is not stable at the ground state, id. 0 Kelvin ( the crystal structure change before and after relaxation, but the energy is still negative) Thus I...
19 February 2023 8,076 7 View
Dear all Gromacs user, I am using Gromacs to run NVT and NVT equilibrium. Before the equilibrium, my input gro file shows all atoms (proteins, Zn, Na and Cl ions, and waters) stayed in the box...
18 February 2023 4,715 1 View