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Questions related to Gromacs
older adukts reason for admisson
07 July 2023 9,997 1 View
The cochlea is small. So I want to know how to get enough and pure RNA.
27 June 2023 2,592 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 7,804 7 View
Hello What is the the concept of MAT-PROP-NORMALIZED in topology optimization in abaqus? What is the variable?
10 June 2023 7,000 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 4,050 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 7,522 1 View
Am using D E Shaw Schrodinger 2022-4 package following the installation i set the environment variable as specified by the instructions However, when i try to use any functions of the package like...
29 May 2023 1,164 0 View
Hi…is there another Library other than system.encryptographyprovider which includes IDEA encryption provider in C# and C ++…?
18 May 2023 4,130 4 View
Are there any forms to display cholesterol in VMD for a pdb file within membrane?
16 May 2023 8,709 1 View
I am encountering issues with building DSM/POPE/POPC/Cholesterol membrane . My job id (if I read my files correctly) is 8388718807. The error states: "CHARMM was terminated abnormally. Please...
12 May 2023 5,220 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 2,967 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 3,554 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 8,405 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 251 2 View
When i collect data of properties of small molecules from public domain,like pKa,solubility and clearance.do i have some methods to evaluate the quality of the datasets before train a machine...
03 May 2023 1,303 1 View
I have prepared conducting polymer nanocomposites in powder form. I tried pelletizing the sample for dielectric studies, but it is cracking. I would like to know if PVA can be used as a binder in...
25 April 2023 9,174 2 View
When generating C code from ST code, MatIEC compiler creates a file with variables for debugging.
23 April 2023 9,326 0 View
I need to calculate the crystallinity of a compound by DSC
13 April 2023 1,826 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 5,664 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 3,102 2 View
How can I use amber forcefield in materials studio?
07 April 2023 2,537 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 5,897 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 5,881 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 6,015 1 View