[gmx-users] Re: diffusion constant level off

[Justin Lemkul]

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 your problem.

-Justin

> 2013/3/28 Justin Lemkul <jalemkul at vt.edu>
>
>> On Thu, Mar 28, 2013 at 9:59 AM, 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?
>>>
>>>
>> I see no evidence for a bug, and you should avoid such speculation unless
>> you know exactly how the program should behave. Only then, after an
>> analysis of known quantities or behavior, can we discuss bugginess. Do you
>> know how g_msd works? Do you know what all of the flags are doing, or are
>> you just making adjustments hoping for clarity? You may find the following
>> post very illuminating:
>>
>> http://lists.gromacs.org/pipermail/gmx-users/2010-July/052512.html
>>
>> -Justin
>>
>>
>>> 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
>>> --
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>>
>>
>>
>> --
>>
>> ========================================
>>
>> Justin A. Lemkul, Ph.D.
>> Research Scientist
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540)
>> 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
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>
>
>

-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================