[gmx-users] Re: diffusion constant level off

[David van der Spoel]

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