Manoj Rana

11 Questions 5 Answers 0 Followers

Questions related from Manoj Rana

How to do pca analysis of c-alpha atom of the protein?

i m interested in pca analysis of c-alpha atoms in gromacs for that i used the following gmx_mpi covar -s mdca.tpr -f mdca.xtc -o eigenvalca.xvg -v eigenvecca.trr -av average.pdb -n index.ndx but...

31 July 2024 1,564 1 View

Getting this error : gmx_mpi': corrupted size vs. prev_size: 0x0000000001d1b320 ***?

i am using the trjconv command in gromacs gmx_mpi -debug trjconv -s md.gro -f md.xtc -o utr.xtc -fit rot+trans and after few steps i got the error gmx_mpi': corrupted size vs. prev_size:...

18 July 2024 6,187 1 View

WARNING: FENE bond too long: 1 7 8 32968539.141547877 (src/MOLECULE/bond_fene.cpp:83) ERROR on proc 0: Bad FENE bond (src/MOLECULE/bond_fene.cpp:85)?

# Polymer chain simulation with FENE and LJ potential in NVT ensemble # Initialization units lj # Use LJ units atom_style bond # Atoms and bonds boundary p p...

17 April 2024 5,804 0 View

Bond broken in fene potential?

i simulating a single chain polymer with 10 particle with fene and lj but if i increase the no of particle my bonds are being broken . im using parameters as below 20 50000.0 0.1 1000.0 1.0...

16 April 2024 2,720 0 View

How to calculate the center of mass coordinate of the protein in gromacs?

i want to find center of mass coordinate of the protein,for that i using the following command gmx_mpi traj -f md_noPBC.xtc -s md.tpr -com -ox com.xvg -pbc but i m not getting satisfactory...

05 March 2024 705 4 View

I m getting less no of data points while using gmx vanhove command?

gmx_mpi vanhove -s md.tpr -f md_noPBC.xtc -or vanhove.xvg -n index.ndx 0 200 0.01 0 0.02 0 0.03 0 0.04 0 0.05 0 0.06 0 0.07 0 0.08 0 0.09 0 0.1 0 why this command is only giving this...

02 March 2024 428 1 View

Is there any way to calculate fs(k,t) in gromacs?

I want to calculate fs(k,t) from gromacs.is there any way how to do that

01 March 2024 3,825 1 View

How to generate md.trr file in gromacs ?

i want to produce a md.trr file rather than a md.xtc file i'm using the following command gmx_mpi mdrun -ntomp 12 -v -s md.tpr -o md.trr after producing md.tpr file

28 February 2024 8,080 1 View

How to calculate msd in gromacs?

i m calculating msd for 2rvd(chignolin) by my self made c code but the results are not as expected. so i want if there is any way to calculate msd in gromacs.also my msd is getting saturated after...

27 February 2024 7,850 1 View

How to find trejectory of solvent in gromacs?

i want to find the trejectory of the solvent gromacs, any idea how would i do that

27 February 2024 8,023 4 View

Relaxation mode analysis

I m working on proteins and polymers and I m very confused about this concept of relaxation mode analysis can anyone help

01 January 1970 6,015 4 View