[gmx-users] Extending Simulation

[bharat gupta]

Thank you Mark and Chandan. I found two files traj.xtc and traj.trr that
were written for the extended simulation and I concatenated those
respective files with the previous trajectories.

Sorry to ask this here, but I have posted questions regarding PCA analysis
2 days back and I have not got any reply from the user-list. So, if you
people can help me out with this , it will of great help. Here's the query
that I posted for the PCA analysis ..


I want to perform the dihedral PCA for two residues of a turn region in a
protein i.e 4 dihedral angles. I have created an index file for the atoms
constituting phi and psi angles for those two residues. But I don't
understand what has to be written in covar file .. According to manual it
says "covar.ndx, which necessarily contains one group of atom 1 to
integer(2*N/3), where N is the number of dihedral angles". This means that
covar should contain 1 2 3 (for 4 dihedrals). Here's teh steps that I
followed till now.

1. Make an index file for residues 116 , 117 phi-psi angles . Here's its
contents :
[phi-psi-116-117]
1797 1799 1801 1809
1799 1801 1809 1811
1809 1811 1813 1816
1811 1813 1816 1818
2. used _angle -f mdrun.xtc  -n index-dihedral.ndx -or dangle.trr -type
dihedral -b 5000 -e 10000
3. trjconv -s mdrun.tpr -f dangle.trr -o resiz.gro -n covar.ndx -e . Here's
the content for resiz.gro file :
Generated by trjconv : Protein in water t=   0.00000
    3
    1ALA      N    1  -0.234   0.972   0.083
    1ALA     H1    2   0.997  -0.944  -0.329
    1ALA     H2    3  -0.017  -1.000   0.000
   2.00000   2.00000   2.00000
Why there is alanine here in this file ??

Thanks in advance for help

===========
BHARAT





On Sat, Nov 23, 2013 at 12:49 AM, Mark Abraham <mark.j.abraham at gmail.com>wrote:

> Reading the .log file is sometimes useful ;-) There you will find what
> inputs mdrun actually had, and thus decided to do!
>
> Mark
> On Nov 22, 2013 4:11 PM, "Chandan Choudhury" <iitdckc at gmail.com> wrote:
>
> > Dear Bharat,
> >
> > You can check the time stamp of the trajectory. You can get an idea
> whether
> > anything was written on it or not.
> >
> > Chandan
> >
> >
> > --
> > Chandan kumar Choudhury
> > NCL, Pune
> > INDIA
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