- 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
- 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
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 n
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
The simplest advice is to increase sampling.
> Please see plot:
> http://imageshack.us/photo/my-images/35/diffusion.png/
>
> 2013/3/28 Justin Lemkul
>
> > On Thu, Mar 28, 2013 at 9:59 AM, Ahmet yıldırım
> > wrote:
> >
> > > Dear users,
> > >
> > > Again, I have strange results (for 10,50,100,
Please see plot:
http://imageshack.us/photo/my-images/35/diffusion.png/
2013/3/28 Justin Lemkul
> On Thu, Mar 28, 2013 at 9:59 AM, Ahmet yıldırım
> 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?
> >
> >
>
On Thu, Mar 28, 2013 at 9:59 AM, Ahmet yıldırım 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 program should beh
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 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?
>
> Co
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 -b
>
> 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
>
>> On 2013-03-28 10:40, Ahmet yıldırım wrote:
>>
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
> On 2013-03-28 10:40, Ahmet yıldırım wrote:
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 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 -trestart
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