[gmx-users] Self Diffusion contant
teklebrh at ualberta.ca
teklebrh at ualberta.ca
Thu Oct 7 18:36:28 CEST 2010
Dear Gromacs,
I have been calculating the self Diffusion constant of my system.
Surfactants in a different solvents of the same volume. After
simulation for 20ns I found the following data for the trajectory of
the mean square displacement.
# D[ TPA] = 0.2039 (+/- 0.0503) (1e-5 cm^2/s)
0 0
2 0.0105286
4 0.0162435
6 0.0212711
8 0.026031
10 0.0307584
12 0.035134
14 0.0393323
16 0.0434628
18 0.0475354
20 0.0516609
-
-
-
-
-
-
920 1.16467
922 1.16756
924 1.1703
926 1.17267
928 1.17383
930 1.17483
932 1.17581
934 1.17754
936 1.17957
938 1.18199
940 1.1829
942 1.18596
944 1.18871
946 1.19099
948 1.19219
950 1.19321
952 1.19445
954 1.19613
956 1.19838
-
-
-
-
-
-
10576 11.7747
10578 11.785
10580 11.7817
10582 11.7833
10584 11.7847
10586 11.784
10588 11.7855
10590 11.7904
10592 11.7926
10594 11.7943
10596 11.8036
10598 11.8141
10600 11.8112
-
-
-
-
-
-
19960 36.4106
19962 36.2607
19964 39.9243
19966 39.7493
19968 39.6744
19970 39.5838
19972 39.6723
19974 39.6374
19976 39.518
19978 39.4935
19980 39.3834
19982 39.1136
19984 42.3888
19986 42.168
19988 42.1337
19990 41.9395
19992 42.0065
19994 42.0993
19996 41.8652
19998 41.8419
20000 41.9419
20002 41.6049
From my data, the graph shows a linear trend until 18ns but as soon
as it reaches around 19, 20ns it dramatically increases the MSD value.
Since the surfactants form aggregation I was expecting the MSD curve
to go down. Is any explanation for that. Why? suddenly increases the
MSD curve. Which is then the correct slop then!
Thank you
Rob
Quoting "Justin A. Lemkul" <jalemkul at vt.edu>:
>
>
> Paymon Pirzadeh wrote:
>> I assumption was that when provide the index file, do_dssp will do the
>> analysis for the protein but prints out the results only for the
>> designated residues. All I wanted was a better resolution on the final
>
> When prompted for only one group, that group is used for calculation
> and output.
>
>> xpm plot to see the secondary structure of the protein at those residues
>> of interest. Any suggestions on how we can increase the resolution of
>> dssp plot and enlarging the axis of residues?
>
> Yes, use an .m2p file to adjust the matrix spacing. This was
> discussed several days ago.
>
>> By the way, what would the option -nice do here?
>>
>
> Likely nothing. Nice levels are irrelevant for most tasks.
>
> -Justin
>
>> Paymon On Wed, 2010-10-06 at 15:29 -0400, Justin A. Lemkul wrote:
>>> Paymon Pirzadeh wrote:
>>>> Justin,
>>>> I produced the index file based on your suggestion, but when I ran the
>>>> do_dssp, a completely different result was spit out comparing to what
>>>> the whole protein analysis had given. Any ideas on why that might have
>>>> happened?
>>>>
>>> That depends on what "completely different" means. I have no
>>> idea. If you're only analyzing a subset of the residues, you're
>>> going to get a discontinuous plot that's probably going to look a
>>> whole lot different from any analysis done on the whole protein.
>>> What's more, if you're only considering small fragments of the
>>> protein, then omitting surrounding residues from the analysis
>>> probably won't permit DSSP to find hydrogen bonding partners that
>>> are necessary to determine the correct secondary structure.
>>>
>>> -Justin
>>>
>>>> Paymon
>>>>
>>>> On Wed, 2010-10-06 at 14:42 -0400, Justin A. Lemkul wrote:
>>>>> Paymon Pirzadeh wrote:
>>>>>> Hello, I want to check the secondary structure of protein at particular
>>>>>> residues. Since dssp needs all main chain atoms, does the
>>>>>> following command
>>>>>> at the make_ndx prompt makes the correct index file?
>>>>> You can answer that yourself by looking at the resulting index file.
>>>>>
>>>>>> 5 | r 1 | r 10-11 |r 14-17 | r 20-21 | r 26-32 | r 42 | r 45
>>>>>>
>>>>> To get these groups to merge, I think you probably need to do 5
>>>>> & r 1 | ...
>>>>>
>>>>> -Justin
>>>>>
>>>>>> (Main chain atom of particular residues). regards,
>>>>>>
>>>>>> Paymon
>>>>>>
>>>>> --
>>>>> ========================================
>>>>>
>>>>> Justin A. Lemkul
>>>>> Ph.D. Candidate
>>>>> ICTAS Doctoral Scholar
>>>>> MILES-IGERT Trainee
>>>>> Department of Biochemistry
>>>>> Virginia Tech
>>>>> Blacksburg, VA
>>>>> jalemkul[at]vt.edu | (540) 231-9080
>>>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>>>>
>>>>> ========================================
>>>>
>>> --
>>> ========================================
>>>
>>> Justin A. Lemkul
>>> Ph.D. Candidate
>>> ICTAS Doctoral Scholar
>>> MILES-IGERT Trainee
>>> Department of Biochemistry
>>> Virginia Tech
>>> Blacksburg, VA
>>> jalemkul[at]vt.edu | (540) 231-9080
>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>>
>>> ========================================
>>
>>
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> --
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