What is the fastest way to extract a single time frame from a large trr file in Gromacs?

I have a very large trr file generate in Gromacs. I need to extract an single time frame in specific time. I know I can do the following: trjconv -f md.trr -s md.tpr -o frame.pdb -dump time But it...

31 December 2014 9,033 4 View

How to convert .pdb in PYMOL to .gro in GROMACS?

Whenever I need to convert a pdb file from PYMOL to GROMACS, the ordering and name of atom inside the residue is different from those inside the default force-field. So whenever I convert a pdb to...

11 December 2014 5,706 11 View

How do you get the potential of protein (excluding solvent) in Gromacs

In gromacs, we can get the potential of the system (including solvent) in .edr file. However, in my case, I need to get the potential of the protein only (excluding solvent). How do I calculate...

07 August 2013 3,671 6 View

error in running a model in Abaqus

Excessive rotation of nodes in node set ErrNodeExcessRotation-Step1

17 August 2021 0 0 View

error in modelling model in Abaqus

Excessive rotation of nodes in node set ErrNodeExcessRotation-Step1

17 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

MD MOE RMSD

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

07 August 2021 0 0 View

MGL tools

20 June 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

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

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

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

flexibility of polymers chain

effect of double bond on the flexibility of polymers

07 April 2021 0 0 View