[gmx-users] problem facing after continuing the trajectory

David spoel at xray.bmc.uu.se
Sun Oct 2 10:21:29 CEST 2005

On Sun, 2005-10-02 at 10:49 +0530, Rahul Karyappa wrote:
> Dear all,
>     I have ran MD run on my system consisting of a polymer chain
> surrounded by ions and water molecules. First I ran MD run for total
> 3ns timesteps. We wanted to look at the radius of gyration behavior
> for the chains having different initial structures of the polymer
> chain. The initial Rg value of the chain was around 2nm and after 3ns
> MD simulation it was around 4-5 nm. 
>   What I did is I continued the trajectory for more 5ns. When I
> calculated the Rg value for the continued trajectory, the value for Rg
> at 3ns timestep was around 2nm. But at the end of the previous run
> (3ns) the value of Rg at 3ns timestep was around 4-5 nm. Why is it
> showing two different values of Rg for the same timestep?
> Looking forward to your kind reply. Thanking you in advance.
Periodic boundary conditions. Run trjconv -pbc whole
> Rahul Karyappa
> NCL, Pune
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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