[gmx-users] Re: diffusion constant level off

[Dr. Vitaly Chaban]

>
> 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 believe the advice was to increase "trestart" and you can decide
yourself how much to increase.

Most likely, your protein deserves better sampling than 10 ns for a
linear diffusion.

Dr. Vitaly Chaban