Simulation
How I use the installed version of Gromacs 2018 from my home directory in CDAC-BRAF server? Please help me out..
08 September 2018 4,068 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 10,177 0 View
Hydrogen bond analysis
06 July 2018 6,521 2 View
gromacs
04 May 2018 2,093 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 417 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 8,871 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 4,146 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 6,403 6 View
what is the command for it???
07 August 2017 7,184 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 7,193 2 View
How to develop investments in renewable energy sources?
08 August 2024 5,112 3 View
I have face this problem anyone help me how to solve this issue ?which is below Fatal error: There are inconsistent shifts over periodic boundaries in a molecule type consisting of 78 atoms. The...
07 August 2024 2,598 1 View
Is it possible to conduct a molecular dynamics simulation to see the effects of a specific carbohydrate on the structure of lipids (e.g., micelle structure)? I am a beginner in this field and plan...
03 August 2024 3,371 3 View
I am using a windows system, what software I should use for hydration shell analysis with molecular dynamics?
02 August 2024 3,143 4 View
Can we patent a process flow diagram developed using a process simulator but no actual cases is carried out? For example consider a process for certain product manufacture where a new process flow...
31 July 2024 781 1 View
Hello. Thanks for your consideration to see my question. Recently, I conducted XPS anaylsis of g-CN that is prepared from thermal polycondensation of DCDA, so-called conventional bulk-g-CN,...
30 July 2024 9,824 2 View
Dear All Gromacs User I would like to restart MD without using checkpint .cpt files? I heard there is a way for acheiveing this. Any input and sugegstions are most welcome. Thanking You Budheswar
29 July 2024 3,084 8 View
I am looking to predict some production for future onshore wind energy production in Portugal, is there any database with info of performances of the existing wind farms in the country? something...
28 July 2024 1,750 1 View
I have different polymer solutions and I hypothesize that water molecules are retained based on the water-polymer interactions, so the amount of free water is less to intercat with drug tablet....
28 July 2024 9,545 6 View
If I want to calculate molecular dynamics (Gromacs), do I first need to optimize the geometry of the molecule? For example, I first draw the molecule in Avogadro, and then what? I guess I can't...
28 July 2024 673 3 View
