I am having difficulty in plotting the histogram.xvg file obtained from REMD using xmgrace. Can I plot it with matlab? if yes please help.
See the answer 'Ignoring header text when using dlmread or similar function', https://www.mathworks.com/matlabcentral/answers/8527-ignoring-header-text-when-using-dlmread-or-similar-function
I am planning to do MD simulation of IDPs using charmm36m force field. The software I am planning to use is GROMACS 2019. Hence, my question is how do I get the charmm36m force field in GROMACS...
01 February 2020 2,698 3 View
I am trying to do PCA from the MD trajectory of a multi-domain protein using GROMACS tools. I am using gmx covar and gmx anaeig for PCA. My protein has many domains, but I would like to focus on...
11 December 2019 1,171 4 View
I am currently simulations a complex containing protein, dsDNA and RNA. The trajectory is generated in Anton2. I would like to visualize and analyze the the trajectory with VMD. Due PBC the...
03 April 2019 2,337 4 View
After about 600ns of my MD run, I notice that my molecule has started interacting with the image. I understand that I should use a larger box length but is it possible for me to continue the MD...
02 March 2019 2,879 4 View
I am running MD simulations with GROMACS 2018. I am planning to run 500ns but I want my trajectories and other output files in five different sets, i.e., filename XXX_100ns. , XXX_200ns.,...
01 February 2019 6,796 4 View
I am using GROMACS2018 with amber14sc_parmbsc1 force field for simulations. I have DNA,RNA,protein,NA,MG and water in my system. I want to analyze my trajectory. the way I have written my...
31 December 2018 7,639 3 View
I have two groups defined in the index file. The group [ protein ] has all protein atoms and the group [ DNA_5 ] has all the atoms of residue id 5 of DNA. I want to calculate the distance between...
09 October 2018 1,882 5 View
My systems contains proteins + Nucleic Acids + Mg2+ ions. First I solvate this using gmx solvate and then I try to neutralize the system using gmx genion with the option "-neutral". However, I see...
03 April 2018 7,964 3 View
I am attaching here two files: 1. XXX_solv_ions.gro : This file was used for energy minimization and the residue (VAL 647) seems perfect here 2. em.gro : This file as obtained after energy...
02 March 2018 2,833 1 View
I have performed MD simulation with RNA (3 strand helix) using GROMACS. During MD-run the strands are separated due to PBC and also broken during PBC. How to "unwrap" or make the molecule...
04 May 2017 6,564 4 View
The paper in question is "Interpolation of Nitrogen Fertilizer Use in Canada from Fertilizer Use Surveys". This paper was very recently published by Agronomy (MDPI). Agronomy has, in the last day...
07 August 2024 9,934 3 View
Program: g_mmpbsa, version 2024.1 Source file: extrn_apbs.cxx (line 152) Fatal error: Failed to execute command: $APBS pybYcUWA.in --output-file=pybYcUW.out
07 August 2024 6,066 0 View
The first pdf file I uploaded had an error. So I uploaded an updated, corrected pdf of that paper with a different pdf name. I dpon't want the old copy to be download or read.
07 August 2024 9,508 1 View
Dear QE-users, In the method where full MS positive mode and PRM mode are used, we always get an incorrect auxiliary gas reading (41 instead of 25). This only happens in this method; other...
06 August 2024 4,953 0 View
Dear Researchers Kindly share JCPDS 65-7246 file Thanks in advance
04 August 2024 5,613 1 View
Hi everyone I need a file with a dirty and clean potato image
04 August 2024 7,199 4 View
How to change the displayed full article text to its corrected version? In the file on the page of the journal where I published the article, there was an error in the text, the table is...
30 July 2024 3,229 2 View
I am new to Micromechanics and having similar problem with understanding the implementation of the formula's. I would appreciate if anyone can guide me on how to go about getting a scalar value...
30 July 2024 969 0 View
Difficulty with permittivitt and Magnetic Permeability Calculations Hello everyone, I have all the parameters related to the calculations of the permittivitty and magnetic permeability...
30 July 2024 5,206 1 View
i m interested in pca analysis of c-alpha atoms in gromacs for that i used the following gmx_mpi covar -s mdca.tpr -f mdca.xtc -o eigenvalca.xvg -v eigenvecca.trr -av average.pdb -n index.ndx but...
30 July 2024 1,607 1 View