17 Questions 26 Answers 0 Followers
Questions related from Urszula Sylwia Uciechowska-Kaczmarzyk
I am trying to run equilibration i gromacs 5.0.7 Implicit solvent. My input file is: ; MD CONTROL OPTIONS integrator = md dt = 0.002 nsteps =...
12 December 2017 6,769 0 View
I am looking for a software for preparing nice (publication) pictures of sequence alignment.
03 March 2016 9,300 8 View
Does anyone know how to build a ssDNA in hairpin conformation? Does anyone know maybe other software where I could do this? Thank you in advance for any suggestions.
02 February 2015 8,426 6 View
I want to run dsDNA-protein MD simulations. I have tried to use top_all36_na.rtf Iprepared a script to run psfgen: package require psfgenresetpsf topology charmm36.nbfix/top_all36_na.rtftopology...
01 January 2015 417 9 View
Is there any fast way to change the DC on CYT for NAMD?
01 January 2015 1,357 2 View
How should I specify it after running make_ndx? for example r259 and DA2(from DNA). Does anyone know?
10 October 2014 4,151 3 View
If yes should I use the same ff as for the dsDNA? Does anyone know?
10 October 2014 5,064 2 View
Is it possible to run RMSD calculations for the part of the protein for example rmsd for AA 45-187? How to specify it using g_rms command?
10 October 2014 3,118 7 View
Does anyone know if there is a tutorial for Computational Alanine Scanning using GROMACS?
10 October 2014 5,842 0 View
Does anyone know how to analyse the plot obtained from gyration? I know what it means but I'm not sure how to use this measure or interpret data? I run MD for a protein in complex with DNA.
10 October 2014 1,612 3 View
I have an xray structure of a dimer protein in complex with DNA. I would like to use available computational methods in order to select amino-acids that are responsible for protein dimerization. I...
08 August 2014 948 4 View
Representatives of this motifs are present in most sequenced members of the eubacterial, UmuC families and the MutS1. I found a paper from 2001 and would like to update the information (they used...
08 August 2014 4,907 2 View
I try to run C-G MD using gromacs. For this purpose I used the martini ff and I follow martini tutprial http://md.chem.rug.nl/cgmartini/index.php/proteins#martini. However on equilibration stage I...
07 July 2014 1,898 4 View
I run MD simulations in GROMACS for 20ns which is 1000000 nsteps using dt= 0.02. I would like to extend it to another 20ns in order to have a complete run for 40ns. How should I proceed? According...
07 July 2014 6,437 20 View
I would like to insert a chain name into my gro file (coarse grained MD)? Is it possible to use editconf or vmd? Any ideas on how to do this?
07 July 2014 7,121 2 View
I have several trajectory files each was rub for 20ns, how to run rmsd analysis? Can I combine them and run one g_rms?
07 July 2014 9,161 3 View
I am working with gromacs and I have got a warning as shown below. Can you please suggest what to do to run my file completely. Please reply as soon as possible. I am awaiting your...
06 June 2014 6,879 10 View
