Hi users,
I would like to calculate diffusion of water molecules in the first
hydration shell (say 0.4nm around protein). I have used trjorder command as:
trjorder -f *.xtc -s *.tpr -o ordered.xtc -r 0.4
Can I directly use
g_msd -f ordered.xtc -s *.tpr
after that to calculate diffusion of water
Hi Pratibha,
Unfortunately, that is not going to work. trjorder puts the closest water
molecule first in the output trajectory. But the closest one at time t need
not be the same as the closest one at time t+dt. So the MSD will be
meaningless.
Cheers,
Tsjerk
On Sun, Aug 17, 2014 at 11:20 AM,
hello Justin
Thank you for your advice, that was really fruitful.
can you kindly tell me how to visualize the molecule which is appearing or
disappearing (lamda 0 to 1, lamda 1 to 0 respectively)?
moving forward i am interested in calculating free energy of reacting mixtures
so could you
How are you making the export GMXLIB? Check that or try putting a copy
of vdwradii.dat
on ./ instead.
Use -debug 1 as Justin suggested and check the debug output for the radius
that are being used by g_sas.
João
On Sun, Aug 17, 2014 at 2:09 AM, Eric Smoll ericsm...@gmail.com wrote:
Hello
On 8/17/14, 12:41 AM, Batdorj Batsaikhan wrote:
Thank you Justin,
It is working but how can I adjust x-axis. My figure y-axis is ok, and x-axis
has not time.
You'll need to post your .m2p file and a link to an image of the output. None
of the settings should be able to remove an axis
On 8/17/14, 10:36 AM, Swapnil Kate wrote:
hello Justin
Thank you for your advice, that was really fruitful.
can you kindly tell me how to visualize the molecule which is appearing or
disappearing (lamda 0 to 1, lamda 1 to 0 respectively)?
Visualize it like you would anything else. As
