John Shultz wrote:
I modified the .mdp file, created a full system tpr, then ran it
through tpbconv, then ran mdrun using the original xtc. It says the
atom numbers don't match.
mdrun -rerun md.xtc -v -s lig.tpr
-------------------------------------------------------
Program mdrun, VERSION 4.0.5
Source code file: md.c, line: 859
Fatal error:
Number of atoms in trajectory (37655) does not match the run input file (65)
-------------------------------------------------------
This time it appears that you have saved your whole system rather than the some
other subset (ligand only?). Check your xtc-grps to see what was written.
-Justin
On Sun, May 23, 2010 at 5:16 PM, Justin A. Lemkul <jalem...@vt.edu> wrote:
John Shultz wrote:
Justin,
Only problem is I need to change this parameter
energygrps
to track the energy on specific groups in the simulation. Is there a
way to modify the simulation parameters to track these energies?
Modify the .mdp file the way you need to, create a full-system .tpr file,
then run it through tpbconv.
-Justin
On Sun, May 23, 2010 at 5:07 PM, Justin A. Lemkul <jalem...@vt.edu> wrote:
John Shultz wrote:
I want to run a subset of an original trajectory. I know how to get
the tpr consisting of the subset. How do I modify the simulation with
a new mdp file and then run the mdrun? I was referencing these
instructions
If you have a .tpr file, then the .mdp file is a step backwards. You
don't
need it.
Assuming you want to do some sort of re-run procedure, you simply have to
run:
mdrun -s subset.tpr -rerun original.xtc
(where original.xtc is your trajectory file that contains the same subset
of
atoms as subset.tpr)
-Justin
http://manual.gromacs.org/current/online/tpbconv.html
3nd. by creating a tpx file for a subset of your original tpx file,
which is useful when you want to remove the solvent from your tpx
file, or when you want to make e.g. a pure Ca tpx file. WARNING: this
tpx file is not fully functional.
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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