29 Questions 62 Answers 0 Followers
Questions related from Angana Ray
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...
02 February 2020 2,636 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...
12 December 2019 1,124 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...
04 April 2019 2,249 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...
03 March 2019 2,828 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.,...
02 February 2019 6,721 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...
01 January 2019 7,570 3 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.
10 October 2018 7,233 1 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...
10 October 2018 1,821 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...
04 April 2018 7,913 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...
03 March 2018 2,760 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...
05 May 2017 6,518 4 View
I did simulation using NAMD and wrapall = on option. While saving the coordinates in pdb format from the trajectory format, I want to unwrap the molecule.
08 August 2014 1,830 6 View
On performing NBO analysis (Pop=nboread, $nbo bndidx $end ) using g09, the matrix showing bond orders has some negative values. What does that signify?
07 July 2014 7,121 11 View
I have done SMD of telomeric quadruplex DNA using NAMD software, GBIS implicit solvent model and CHARMM-27 ff. I have pulled the center of mass of the 1st base keeping center of mass of the last...
02 February 2014 4,368 1 View
I have done SMD of a protein using NAMD and CHARMM ff. I would like to calculate PMF using bio3d-package of R.
12 December 2013 363 2 View
I have already started quantum studies on graphene sheets. I have optimized graphene and GO sheets using DFT and b3lyp,wb97xd basis sets. Apart from optimization I am a little confused as which...
12 December 2013 2,033 2 View
I am trying to study how a graphene sheet is cut upon oxidation using theoretical methods (mainly using Gaussian, g09 software). I am confused about how the process actually takes place. Is it...
12 December 2013 850 2 View
I am doing SMD of protein using NAMD with constant velocity pulling. In order to do the simulation, we have to specify the smd-atom (the atom to which the dummy atom is attached and then pulled)....
11 November 2013 8,725 1 View
I have done SMD of protein at applying constant velocity using NAMD software and CHARMM ff. Since, this is my first time in performing Steered MD, I am not sure as to should I do umbrella sampling...
11 November 2013 7,884 3 View
I have done SMD of protein using CHARMM ff and NAMD software. I want to do an umbrella sampling for the protein using NAMD as it is important to do umbrella sampling while doing SMD. Can anyone...
11 November 2013 6,835 1 View
I am doing SMD of protein using NAMD and CHARMM ff. I have an output file which gives the 3 components of force applied and coordinates of the atom on which force is applied for various snapshots....
11 November 2013 3,044 5 View
I want to do Steered Molecular Dynamics with umbrella sampling. Can anyone help me with examples or scripts ?
11 November 2013 4,805 1 View
The electric potential given in the output of g09 job is in atomic units, how can that be converted into SI-units
09 September 2013 1,175 0 View
While using keyword Pop=ESP in the input file for running g09, the job gets terminated showing an error message. It happens only when the molecule has potassium atom in it. The error message is...
09 September 2013 9,490 8 View
I am trying to strudy force induced unfolding of protein by constant force SMD Simulation using NAMD. I have used GBIS, because the water model is not possible. I see that my protein completely...
09 September 2013 5,102 1 View
In order to do MD Simulation using NAMD software and CHARMM FF, I have used implicit water model and diel=4 but since my molecule is charged (DNA), I would like to know if I can use explicitions...
09 September 2013 8,516 10 View
How can we apply a constant force on a single atom for carrying out MD simulation using NAMD?
09 September 2013 9,118 7 View
I was curious as how to give in the amout of force in the conf file used for running NAMD simulation.
09 September 2013 4,307 2 View
Molecular Dynamics Simulation is done by CHARMM and Constant Force is applied on one atom each of the two terminal bases.
09 September 2013 8,106 3 View
