[gmx-users] g_rmsf

[Tsjerk Wassenaar]

Hi Pooja,

Try to get a grip on the file types and what they contain. A .cpt file
is a checkpoint file containing a single configuration. Not much
fluctuation to expect there. This sort of analysis only makes sense
for a trajectory, or at least an ensemble of structures. Try the .xtc
or the .trr file.

Cheers,

Tsjerk

On Sat, Jul 17, 2010 at 7:55 PM, Sai Pooja <saipooja at gmail.com> wrote:
> Hi,
> I am running an npt simulation for a protein in water. For more than 50% of
> the residues the backbone atoms have been restrained by applying
> posrestraints. I ran g_rmsf to check if the pos-restraints were working
> well. When I do this selecting 'backbone' from the groups menu, my rmsf file
> gives 'nan' for certain residues:
> # This file was created Sat Jul 17 13:40:21 2010
> # by the following command:
> # ../../gromacsnew/bin/g_rmsf -f npt1.cpt -s npt1.tpr -b 0 -e 80 -o
> rmsf2_npt1.xvg -od rmsd2_npt1.xvg -res
> #
> # g_rmsf is part of G R O M A C S:
> #
> # GROup of MAchos and Cynical Suckers
> #
> @    title "RMS fluctuation"
> @    xaxis  label "Residue"
> @    yaxis  label "(nm)"
> @TYPE xy
>     1      nan
>     2      nan
>     3   0.0002
>     4   0.0000
>     5      nan
>     1   0.0002
>     2      nan
>     3      nan
>     4   0.0001
>     5      nan
>     6   0.0001
>     7      nan
>     8      nan
>     9   0.0000
>    10   0.0002
>    11      nan
>    12      nan
>    13      nan
>    14      nan
>    15   0.0000
>    16      nan
>    17   0.0001
>    18   0.0002
> Does this mean that the simulations are not working properly? Does this
> problem occur frequently due to the way the simulation parameters haev been
> set?
> Pooja
> --
> Quaerendo Invenietis-Seek and you shall discover.
>
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>



-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
Groningen Institute for Biomolecular Research and Biotechnology
University of Groningen
The Netherlands