[gmx-users] RE: How to output a single index group

[Vitaly Chaban]

> I am running a simulation of 50000 time steps and am trying to avoid setting
> nstxtcout = 1 or nstxout = 1.  The file size becomes unmanageable if I set
> either of these two parameters to 1.  I do not need the coordinates for all
> atoms in the system, just the alpha carbons, which are grouped in the index
> file, but I do need coordinates for each time step.  Is there any way of
> specifying in the parameter file to only output the coordinates for the alpha
> carbons?  Thanks!

 See xtc-grps


 Start the run with
 grompp -n index.ndx


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Vitaly V. Chaban, Ph.D.(ABD)
School of Chemistry
V.N. Karazin Kharkiv National University
Svoboda sq.,4, Kharkiv 61077, Ukraine
email: chaban at univer.kharkov.ua,vvchaban at gmail.com
skype: vvchaban, mob.: +38-097-8259698