- Expected values are estimated. For example İf the structure is reach to
converge at last 100 ns ( all simulation time is 200 ns), then in theory,
diffusion coefficients will dont change at last 100 ns.
-I have only one diffusion coefficient for each 10 ns. I have 20 diffusion
coefficients during
- Expected values are estimated. For example 輋 the structure is reach to
converge at last 100 ns ( all simulation time is 200 ns), then in theory,
diffusion coefficients will dont change at last 100 ns.
-I have only one diffusion coefficient for each 10 ns. I have 20 diffusion
coefficients
Dear users,
This time, I calculated the diffusion coefficients of protein for each 10
ns of the simulation providing a total simulation time of 200 ns.
g_msd -f traj.xtc -s topol.top -o msd1.xvg -trestart 20 -beginfit -1
-endfit -1 -b 0 -e 1
g_msd -f traj.xtc -s topol.top -o msd2.xvg
On 2013-03-28 10:40, Ahmet yıldırım wrote:
Dear users,
This time, I calculated the diffusion coefficients of protein for each 10
ns of the simulation providing a total simulation time of 200 ns.
g_msd -f traj.xtc -s topol.top -o msd1.xvg -trestart 20 -beginfit -1
-endfit -1 -b 0 -e 1
g_msd
Dear Prof.Spoel,
if I do as you said, I will get only one diffusion coefficient. I want to
calculate one diffusion coefficient for each 10
ns of the simulation time of 200 ns. That is, I want to get 20 diffusion
values.
2013/3/28 David van der Spoel sp...@xray.bmc.uu.se
On 2013-03-28 10:40,
if I do as you said, I will get only one diffusion coefficient. I want to
calculate one diffusion coefficient for each 10
ns of the simulation time of 200 ns. That is, I want to get 20 diffusion
values.
2013/3/28 David van der Spoel sp...@xray.bmc.uu.se
On 2013-03-28 10:40, Ahmet yıldırım
Dear users,
Again, I have strange results (for 10,50,100,150,200 ns). I am wondering,
is there a bug with g_msd?
Commands for trestart to 20 ps:
g_msd -f traj.xtc -s topol.top -o msd1.xvg -trestart 20 -beginfit -1
-endfit -1 -b 0 -e 1
g_msd -f traj.xtc -s topol.top -o msd2.xvg -trestart 20
perhaps, you could make a plot??
it is difficult to understand what you are speaking about.
Dr. Vitaly Chaban
On Thu, Mar 28, 2013 at 2:59 PM, Ahmet yıldırım ahmedo...@gmail.com wrote:
Dear users,
Again, I have strange results (for 10,50,100,150,200 ns). I am wondering, is
there a bug
On Thu, Mar 28, 2013 at 9:59 AM, Ahmet yıldırım ahmedo...@gmail.com wrote:
Dear users,
Again, I have strange results (for 10,50,100,150,200 ns). I am wondering,
is there a bug with g_msd?
I see no evidence for a bug, and you should avoid such speculation unless
you know exactly how the
Please see plot:
http://imageshack.us/photo/my-images/35/diffusion.png/
2013/3/28 Justin Lemkul jalem...@vt.edu
On Thu, Mar 28, 2013 at 9:59 AM, Ahmet yıldırım ahmedo...@gmail.com
wrote:
Dear users,
Again, I have strange results (for 10,50,100,150,200 ns). I am wondering,
is there a
The simplest advice is to increase sampling.
Please see plot:
http://imageshack.us/photo/my-images/35/diffusion.png/
2013/3/28 Justin Lemkul jalem...@vt.edu
On Thu, Mar 28, 2013 at 9:59 AM, Ahmet yıldırım ahmedo...@gmail.com
wrote:
Dear users,
Again, I have strange results
On 3/28/13 5:32 PM, Ahmet yıldırım wrote:
Please see plot:
http://imageshack.us/photo/my-images/35/diffusion.png/
How did you come up with your expected values? What does the original msd.xvg
plot look like? It should be basically linear. If it's not, then you have
found the source of
On 3/28/13 7:56 PM, Dr. Vitaly Chaban wrote:
The simplest advice is to increase sampling.
I think the OP needs to describe what the system is in greater detail. For a
simple liquid, I would opine that 200 ns is normally vast overkill. For a
membrane, it may not be enough. There's just
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