Hi,
Measuring a root mean square deviation requires knowing what conformation
you want to measure a deviation from, which doesn't have to come from any
tpr, either. Preferably you should know what you'll learn from that
measurement, too.
Mark
On Wed, 25 Jan 2017 09:41 leila karami
Dear Justin and Erik,
Thanks for your answers.
How to resolve my problem? How to obtain a reasonable RMSD curve from
10 consecutive MD runs? How to make an appropriate tpr for calculating RMSD?
Best,
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Dear Leila,
The RMSD is, by default, calculated with respect to the coordinates in the tpr
file, which is why you get different results with different tprs. Which one to
choose depends on exactly what you want to measure.
Kind regards,
Erik
__
Erik Marklund, PhD
Dear Justin,
Thanks for your answer.
> If you use gmx convert-tpr to simply change the number of steps
> (much easier and cleaner!)
Based on your suggestion, I used following command to extend first tpr
to all steps.
gmx convert-tpr -f final.xtc -s md1.tpr -n index.ndx -o new.tpr -extend
On 1/23/17 11:10 AM, leila karami wrote:
Dear gromacs users,
About the concatenation trajectory files, I have a question.
I did 10 MD simulations (each section 10 ns). Now, I want to concatenate
all of the trajectories and determine RMSD on whole trajectory. To do this,
I used the following
Dear gromacs users,
About the concatenation trajectory files, I have a question.
I did 10 MD simulations (each section 10 ns). Now, I want to concatenate
all of the trajectories and determine RMSD on whole trajectory. To do this,
I used the following command:
gmx trjcat -f md1.trr md2.trr
