[gmx-users] Re: diffusion constant level off

[Dr. Vitaly Chaban]

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 <ahmedo047 at 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?
>
> 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 10000
> g_msd -f traj.xtc -s topol.top -o msd2.xvg -trestart 20 -beginfit -1 -endfit
> -1 -b 10000 -e 20000
> g_msd -f traj.xtc -s topol.top -o msd3.xvg -trestart 20 -beginfit -1 -endfit
> -1 -b 20000 -e 30000
> ...
> g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 20 -beginfit -1
> -endfit -1 -b 190000 -e 200000
>
> Commands for trestart to 1000 ps:
> g_msd -f traj.xtc -s topol.top -o msd1.xvg -trestart 1000 -beginfit -1
> -endfit -1 -b 0 -e 10000
> g_msd -f traj.xtc -s topol.top -o msd2.xvg -trestart 1000 -beginfit -1
> -endfit -1 -b 10000 -e 20000
> g_msd -f traj.xtc -s topol.top -o msd3.xvg -trestart 1000 -beginfit -1
> -endfit -1 -b 20000 -e 30000
> ...
> g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 1000 -beginfit -1
> -endfit -1 -b 190000 -e 200000
>
>
> D1 (cm^2/s):Diffusion for trestart to 20 ps
> D2 (cm^2/s):Diffusion for trestart to 1000 ps
> Time (ns) D1 D2
> 10 0.1616 0.1091
> 20 0.0735 0.0679
> 30 0.0775 0.0705
> 40 0.1097 0.1189
> 50 0.1471 0.1436
> 60 0.0468 0.048
> 70 0.0667 0.0652
> 80 0.0727 0.086
> 90 0.0664 0.0707
> 100 0.1336 0.114
> 110 0.0899 0.0841
> 120 0.0572 0.0598
> 130 0.0506 0.0482
> 140 0.0723 0.0767
> 150 0.1466 0.1439
> 160 0.0703 0.0601
> 170 0.081 0.0853
> 180 0.0278 0.027
> 190 0.1121 0.1024
> 200 0.3136 0.2981
>
>
> 2013/3/28 Dr. Vitaly Chaban <vvchaban at gmail.com>
>>
>> >
>> > 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
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>
>
>
>
> --
> Ahmet Yıldırım