MD simulation
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html
How I use the installed version of Gromacs 2018 from my home directory in CDAC-BRAF server? Please help me out..
08 September 2018 3,934 1 View
I'm using DSSP 2.0.4. command I used: dssp.exe -i 6NUL.pdb -o 6NUL.dssp what it is the next command to get the image file? Please give me suggestion..
07 August 2018 10,024 0 View
Hydrogen bond analysis
06 July 2018 6,357 2 View
gromacs
04 May 2018 1,983 0 View
I have taken The Bioinformatics Resources & Applications Facility (BRAF) at C-DAC. But donot know how to use it for MD simulation of protein-ligand complex using Gromacs program. Could...
04 May 2018 212 6 View
How can I transfer my files from my university server to BRAf server to perform MD simulation and how can I use environment module ??
03 April 2018 8,735 1 View
Program gmx mdrun, VERSION 5.1.2 Source code file: /build/gromacs-z6bPBg/gromacs-5.1.2/src/gromacs/mdlib/constr.cpp, line: 555 Fatal error: step 12: Water molecule starting at atom 61920 can not...
03 April 2018 3,933 0 View
I am follow this tutorial http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html In my case, protein with ligand simulated for 3ns. But after simulation the...
10 November 2017 6,296 6 View
what is the command for it???
07 August 2017 7,057 1 View
There is zinc in a catalytic site. So, I merge Protein_Zn_Ligand by using command: gmx make_ndx -f em.gro -o index.ndx > 1
07 August 2017 6,919 2 View
When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.
16 June 2021 0 0 View
Hi, I am using GROMACS 5.1.4 to simulate water in contact with a surface. I am only interested to calculate some properties of water near the surface. Let's say at a distance of x nm from the...
03 March 2021 9,989 2 View
I am on the lookout for the Enhanced Yellow Fluorescent Protein (Aequorea victoria) DNA sequence. Does anyone know where I can find it? Thank you in advance
03 March 2021 3,568 1 View
What's the best way to measure growth rates in House sparrow chicks from day 2 to day 10? Since, the growth curve from day 2 to 10 won't be like the "Logistic curve" it might not follow logistic...
03 March 2021 1,401 3 View
Hello, I'm fairly new to ARENA and I have the following problem: I have two queues in which, in each queue, a different order type arrives (both having an arrival rate of exponential 10). Order...
02 March 2021 2,431 3 View
Hello, I have a mechanism where air rises due to convective flows. In this simulation, nothing is driving the air except this. I understand that the Boussinesq approximation only works for small...
02 March 2021 4,910 3 View
Actually, I am running cfd simulation for a heat exchanger which has two fluids one hot and other one is cold fluid. there is a solid domain between them, which I removed and instead I have used...
01 March 2021 9,537 2 View