The electric potential given in the output of g09 job is in atomic units, how can that be converted into SI-units
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
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.
09 October 2018 7,296 1 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
Hello experts, Does anyone know any free software about retention index prediction ?
08 August 2024 7,403 2 View
I am interested to know the behavior of dyes toward light. Specifically, Blue dyes re-emit the spectrum, especially from the green zone (known as principal in LED lamps, and blue dyes are known...
05 August 2024 3,290 1 View
Molecular docking software/ websites?
02 August 2024 8,704 7 View
I'm trying to perform a frequency calculation using Gaussian via MOBAXterm. The output shows no errors, however, there's no frequency as a result on gausview. The option "vibrations" is not...
31 July 2024 631 4 View
I created a file with my outgroup and ingroup species using Beauti, ran it in BEAST, viewed it in Tracer, and then used TreeAnnotator to create a file that I imported into RASP. Could someone...
28 July 2024 2,979 1 View
How can we calculate the percentage of configuration interaction (CI) in the UV output data of the Gaussian program? for example: Excited State 17: Singlet-A 5.1359 eV 241.41 nm...
28 July 2024 9,165 2 View
I am reaching out to seek your valuable advice and recommendations regarding the best software tools to use for this research. Specifically, I am looking for software with a user-friendly...
22 July 2024 3,794 1 View
Hey all, I need help testing for multivariate outliers using STATA for my master thesis. The literature recommends the Minimum Covariance Determinant (MCD) (Verardi & Dehon, 2010). I found the...
22 July 2024 8,821 2 View
Dear Researchers, My question is associated with the "MDCI" method in Orca. Please let me clarify my question using a simple example: Suppose we are going to perform CBS extrapolation using "!...
21 July 2024 1,632 0 View
Serotonin (5-hydroxytryptamine, 5-HT) is predominantly known as a neurotransmitter in the central nervous system (CNS), where it plays a crucial role in mood regulation, gastrointestinal motility,...
20 July 2024 3,925 5 View