Hi Steve
Thanks for the info.
But I am not very sure how to do that.
When I give the input command as
dump 1 all custom poly.trj tag type x y z
dump_modify 1 image yes
it exits with an error message
illegal dump_modify command.
Can you please be more explicit in explaining this.
Can I use pizza.py dump tool only I f I did this or can I still use it if I just dumped the coordinates (unscaled).
Also, the doccumentation for the pizza.py dump tool is not clear to me. Can you please take some time out to explain in steps how to go about doing this. I’ve been breaking my head on this for a while now and I think any help from you would be my last resort.
Thanks so much
Venkat
Hi Venkat,
I believe you can't use dump_modify with the custom style, since
everything can be selected to write out. What you want is
dump 1 all custom poly.trj tag type x y z ix iy iz
Anyway, instead of using unwrapped coordinates to compute the properties
you are interested in (radius of gyration, end to end distance), you can
use the minimum image convention to compute all distances, since
presumably none of your chains spans more than half a box length
(otherwise you'll have strange correlations as the chain will be
interacting with itself). See domain.cpp, in the function
void Domain::minimum_image(double *dx, double *dy, double *dz), to see how
this is calculated.
Naveen
Hi Venkat,
I think the error is because you are not saying how often you want the program to dump the trajectory info.
Let's say you want to dump x y z every 1000 steps, it should be:
dump 1 all custom 1000 poly.trj tag type x y z ix iy iz