Dear Gromacs users,
My Gromacs simulation on a protein terminated without any error and major
warning. However, when I see the conformations, I found them broken.
For trajectory conversion, I have used the following commands:
gmx trjconv -s protein-md.tpr -f protein-md.xtc -center -pbc nojump -u
Dear Gromacs Users,
I am trying to simulate a protein dimer using Gromacs-5.1.2. Gromacs
completed successfully
but when analysing the trajectories, the monomers are flying apart and
coming back again!
I used the following Gromacs commands/options:
gmx trjconv -s protein-md.tpr -f protein-md.xtc
Dear Gromacs users/experts
I was doing principal component analysis with a long (1000 ns) MD
trajectory.
I have seen the protein backbone continuous (not fragmented) with the
simulation time. However, the backbone is fragmented in some trajectories
corresponding to some of the eigenvectors! The Gr
Dear Gromacs Users,
I have the following question:
Suppose I repeat a simulation, keeping everything exactly the same.
What will happen to RMSD? Will it be exactly same with the previous run?
If not, then how much variation is expected?
To check this, I ran two independent simulations:
1) upto t
us...@gromacs.org
> Subject: Re: [gmx-users] Variation of distance between 2 CA atoms with
> time
> Message-ID: <5564dbb9.8020...@vt.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
>
> On 5/26/15 8:42 AM, Biplab Ghosh wrote:
> > Dear G
Dear Gromacs Users,
I am new to Gromacs and using Gromacs-5.0.4.
I want to calculate the variation of distance between to
C-alpha atoms in a protein in course of time.
First, I have created a file called: L153_V161.ndx using make_ndx
and the content of the file is:
[ L153 ]
2277
[ V161 ]
2394
Dear All,
I am a beginner in MD and started with Gromacs. I would like to simulate
the dynamics of a homo-dimeric
protein containing 2 Mn atoms at the active site. I would appreciate any
sorts of help in this regards, e.g.,
please share your experience and/or relevant source in the web/published
