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Questions related to Gromacs
Hi every one. I want to read the results from my previous job but i have to create new part (selected DO NOT USE PARTS...) and cant import part. in defining initial state abaqus gives this...
11 February 2023 2,245 0 View
I intend to write articles using experimental drilling data (inputs and outputs) for which I will need an appropriate analysis and prediction method. what is the chance of publishing an isi paper...
03 February 2023 1,056 2 View
Hi I have a martini system of 1642 atoms. Most of them are overlapping. I tried running energy minimization with all sorts of parameter manipulation but system doesn't resolve and crashes. I am...
25 January 2023 9,530 1 View
Dear Experts I need a list of specifications/components list for setting up a Desktop computer to do molecular dynamics simulation. The main purpose is to do Structure Based Drug Design and...
24 January 2023 9,105 3 View
I'm doing the simulation in single method as always. I haven't changed any parameters.
20 January 2023 4,120 0 View
I have done homology modeling using i-tasser. I have successfully done docking for one of protein but after that it is showing error and empty files for rest of them. Same problem with ClusPro.
20 January 2023 8,569 1 View
In order to investigate the process of entering a protein into a cavity of a MOF, I used SMD, In the direction of the z-axis, the protein has entered the cell and exited from the other side. I...
20 January 2023 3,633 2 View
What DFT method is the most accurate for calculating hydrogen bonding? Dispersion correction seems essential to large-system hydrogen bonds, whereas dispersion correction tends to overestimate...
05 January 2023 7,267 3 View
After selecting the residues of the protein for flexible docking, when I click on "Choose Torsions In Currently Selected Residues", under the " Flexible Residues" tab, I get this error:...
29 December 2022 2,359 1 View
Hello, I need to build a polymer molecule for my molecular dynamics simulation. The target molecule is a random polymer composed of two monomers randomly connected with each other. I know...
14 December 2022 1,334 8 View
i am trying to do umbrella sampling of 2 AU molecules but whenever I am trying to run the md_pull.mdp file it giving an error : ERROR 1 [file md_pull.mdp]: When the maximum distance from a pull...
23 November 2022 1,297 1 View
There are 80 residues in your selected group dssp cmd='/usr/bin/dssp -i ddWL6jqm 2>/dev/null' Reading frame 0 time 0.000 Back Off! I just backed up ddWL6jqm to ./#ddWL6jqm.1#
22 November 2022 1,800 0 View
On what basis should the Ψ and φ values be selected
21 November 2022 1,006 1 View
Hi everyone, I need to perform MD simulations on a large number of protein-ligand docked complexes (88 or more). Previously, I used Swiss Param website to generate ligand topologies and CHARMM...
03 November 2022 8,554 2 View
Actually, it has been listed in here (https://charmm-gui.org/?doc=archive&lib=csml) with document named as toppar_all36_moreions.str but i could not find it. If anyone has, could you please...
26 October 2022 458 1 View
1. In preparing the MD simulation, an equilibration of about 100 ns is done. After building the pure lipid membrane from CHARMM-GUI, I have 6 equilibration.mdp files and one production.mdp file....
18 October 2022 9,916 4 View
Hello everyone! I want to calculate the polarizability of the ferroelectric phase, the phase transition barrier of my compound. Both at a fixed temperature and a heating process for simulation are...
16 October 2022 8,258 0 View
PatchDock online server for protein-peptide showed in result section: You have uploaded an empty file. The file is not empty inside, all the documents contains are PDB structure. How to solve this...
05 October 2022 3,445 3 View
Hello, I am trying to use PatchDock server. My receptor protein has the following structure: ATOM 1 N GLN 1 35.030 57.410 17.050 1.00 0.00 N ATOM 2 CA GLN...
29 September 2022 3,847 0 View
Water content in IPA is 1.7%. I want to decrease it to less than 0.5%. I have tried simple distillation and also distillation using an entertainer such as ethylene glycol. No positive results were...
10 August 2022 8,046 7 View
Hello expert, I had run my sample (DNA-small molecule) for 50ns. Unfortunately, before it complete, I have electrical problem and my run was stopped. Later, I mistakenly took the wrong md.tpr...
21 July 2022 6,789 0 View
MM/PBSA is done for protein in the membrane system. Can anyone please suggest something?
10 June 2022 2,479 1 View
I have run the production step for a protein-membrane system using Gromacs. But, the relevant stepX.X_production.xtc has not generated so that I can't proceed to the RMSD analysis. How can I fix...
31 May 2022 7,706 3 View
I tried to predict the structure of protein complex by alphafold2 using AlphaFold2_complexes (https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/AlphaFold2_complexes.ipynb) To...
19 May 2022 4,563 0 View