[gmx-users] Re: diffusion constant level off

[Ahmet yıldırım]

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 <spoel at xray.bmc.uu.se>

> 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 10000
>> g_msd -f traj.xtc -s topol.top -o msd2.xvg -trestart 20 -beginfit -1
>> -endfit -1 -b 10001 -e 20000
>> g_msd -f traj.xtc -s topol.top -o msd3.xvg -trestart 20 -beginfit -1
>> -endfit -1 -b 20001 -e 30000
>> ....
>> g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 20 -beginfit -1
>> -endfit -1 -b 190001 -e 200000
>>
>
> Set trestart to 10001 (no restarts), or do one run with
>
> g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 10000
>
>
>
>> I have strange Diffusion results (especially 10,50,100,150,200 ns). How
>> can
>> I fix this problem?
>> Results:
>> Time (ns) D(cm^2/s)
>> 10 0.1616
>> 20 0.0735
>> 30 0.0775
>> 40 0.1097
>> 50 0.1471
>> 60 0.0468
>> 70 0.0667
>> 80 0.0727
>> 90 0.0664
>> 100 0.1336
>> 110 0.0899
>> 120 0.0572
>> 130 0.0506
>> 140 0.0723
>> 150 0.1466
>> 160 0.0703
>> 170 0.081
>> 180 0.0278
>> 190 0.1121
>> 200 0.3136
>>
>>
>>
>> 2013/3/27 Ahmet yıldırım <ahmedo047 at gmail.com>
>>
>>>
>>> Dear users,
>>>
>>> I used the following commands to get diffusion constants (every 10 ns) of
>>>
>> a simulation of 100 ns . The number of frame is 5001 (write .xtc
>> trajectory
>> every 20 ps).  I looked at RMSD vs average structure, RMSD vs starting
>> structure, Radius of gyration, RMSD matrix. This simulation has reached to
>> converge at last 50 ns.
>>
>>> g_msd -f traj.xtc -s topol.tpr -o msd_1.xvg -b 0 -e 10000
>>> g_msd -f traj.xtc -s topol.tpr -o msd_2.xvg -b 10000 -e 20000
>>> g_msd -f traj.xtc -s topol.tpr -o msd_3.xvg -b 20000 -e 30000
>>> ...
>>> g_msd -f traj.xtc -s topol.tpr -o msd_10.xvg -b 90000 -e 100000
>>>
>>> 1.) I used the above commands without the following flags ( -type,
>>>
>> -lateral and -ten). Which diffusion will the above comands give? is it
>> bulk
>> diffusion?
>>
>>> Gromacs manual:
>>> -type:Compute diffusion coefficient in one direction:no, x, y or z
>>> -lateral:Calculate the lateral diffusion in a plane perpendicular to: no,
>>>
>> x, y or z
>>
>>> -ten:Calculate the full tensor
>>> 2.) I plotted diffusions (10 values) as function of time. Diffusions dont
>>>
>> converge. Did I do any steps by mistake?
>>
>>> 3.) From manual:
>>> The diffusion constant is calculated by least squares fitting a straight
>>>
>> line (D*t + c)...
>>
>>> What is (D*t + c)? What are the meaning of D and c?
>>> 4.) What should be "Time between restarting points in trajectory"?
>>>
>>> Thanks in advance
>>> --
>>> Ahmet Yıldırım
>>>
>>
>>
>>
>>
>> --
>> Ahmet Yıldırım
>>
>>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
> --
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-- 
Ahmet Yıldırım