After this command "perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat" which file i used for em in membrane simulation ?

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Can any body know how to use latest version of Gromacs in CDAC-BRAF server..?

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

How can I get image file from .dssp file for secondary structure prediction?

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

How to perform hbond analysis between ligand and catalytic residues of receptor in gromacs ?

Hydrogen bond analysis

06 July 2018 6,357 2 View

How can I simulate docked protein complex with pdb water. As these water molecule important in binding of the molecule ?

gromacs

04 May 2018 1,983 0 View

MD simulation of protein-ligand complex using the Gromacs program available at The Bioinformatics Resources & Applications Facility (BRAF) at C-DAC?

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 to do simulation on BRAF server??

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

How to correct "step 12: Water molecule starting at atom 61920 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate" ?

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

How to put constraint in the receptor ligand interaction during MD simulation in Gromacs?

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

How to get receptor- ligand binding energy graph in gromacs after successful md run?

what is the command for it???

07 August 2017 7,057 1 View

Problem with make_ndx command in protein- ligand MD simulation.

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

MD MOE RMSD

How to calculate the RMSD values for a MD simulation using MOE?

07 August 2021 0 0 View

MD MOE RMSD

How to calculate the RMSD values for a MD simulation using MOE?

07 August 2021 0 0 View

fatal error

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

fatal error

16 June 2021 0 0 View

fatal error

16 June 2021 0 0 View

fatal error

16 June 2021 0 0 View

What kind of fluid could I use for a pitfall trap that also does not invalidate molecular testing?

Hi, I want to start testing pitfall trap to obtain ants samples, but I need to conduct molecular analysis on those insects. So, what kind of fluid can I use? Ethanol expires too early and I need...

03 March 2021 5,978 5 View

Arena simulation - how do i model the following model in ARENA (see description) (new to ARENA)?

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

Why are the velocities so high in my Boussinesq approximation Fluent simulation?

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

How to repeat an operation on an atom selection for multiple times in PyMol?

Hi, I am trying to construct a multi-layer fibril structure from a single layer in PyMol by translating the layer along the fibril axis. For now, I am able to use the Translate command in PyMol...

02 March 2021 4,569 4 View