Thank you, My intention is mainly to compare the MSDs of the trajectory and not the diffusion as such. The paper I mentioned have used a tetramer for the similar analysis. Hence I wanted to know whether the values I obtained is sensible.
Thank you Kavya On Thu, Feb 7, 2013 at 7:25 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 2/7/13 7:08 AM, Kavyashree M wrote: > >> Dear Sir, >> >> Yes it is the same protein. Initially I had not superposed the >> structures in the trajectory. But this time I calculated the msd >> on a superposed trajectory (of the same simulation). the simulation >> is carried out on a dimer for 50ns using OPLS-AA and TIP4P water >> model. Using Gromacs4.5.3. >> If any other information is required Please let me know. >> >> > The specific suitability of a protocol is dependent upon what you believe > to be correct for your system based on precedent and chemical knowledge. > Also be aware that post-processing of the trajectory to superimpose frames > defeats the purpose of measuring diffusion - if you re-center or > superimpose your structures, it's not diffusing! Dealing with a dimeric > protein may be a challenge for which g_msd wasn't designed, so I don't know > if there's an easy solution here. Perhaps someone else can suggest > something. > > -Justin > > Thank you >> Kavya >> >> On Thu, Feb 7, 2013 at 5:28 PM, Justin Lemkul <jalem...@vt.edu> wrote: >> >> >>> >>> On 2/7/13 6:49 AM, Kavyashree M wrote: >>> >>> Dear Sir, >>>> >>>> Thank you for the reply, >>>> >>>> It does not cross the boundary. I made the trajectory >>>> so that the dimers are together. >>>> >>>> I again calculated on a superposed trajectory, Then I >>>> got MSDs in the range of 0.01 to 0.15nm^2. But this >>>> is still higher than the value mentioned in the paper or >>>> is this acceptable? >>>> >>>> >>>> Are you studying the same protein? Given sparse detail in an email >>> thread, not knowing whether the simulations were done correctly or for >>> sufficient time, no one can assess correctness here. >>> >>> -Justin >>> >>> On Thu, Feb 7, 2013 at 4:54 PM, Justin Lemkul <jalem...@vt.edu> wrote: >>> >>>> >>>> >>>> >>>>> On 2/6/13 11:49 PM, Kavyashree M wrote: >>>>> >>>>> Dear users, >>>>> >>>>>> >>>>>> Since I am getting the mean square displacements in terms of >>>>>> several nm^2. I doubt it is wrong. Could anyone please explain >>>>>> me the solution for this. I checked the structure it is not denatured, >>>>>> In addition I used -rmcomm in order to remove the COM movements. >>>>>> >>>>>> >>>>>> Sounds like a PBC issue. Does your dimer split across periodic >>>>>> >>>>> boundaries? If it does, then your MSD is going to go through the roof >>>>> because it's measuring the MSD of the whole protein. >>>>> >>>>> -Justin >>>>> >>>>> On Wed, Feb 6, 2013 at 3:35 PM, Kavyashree M <hmkv...@gmail.com> >>>>> wrote: >>>>> >>>>> >>>>>> Dear users, >>>>>> >>>>>> >>>>>>> I have a very basic question in MSD calculation. >>>>>>> g_msd calculation on a protein dimer (~237 aa each) >>>>>>> trajectory gave a plot of msd, with the values ranging >>>>>>> between 1 to 14nm^2. >>>>>>> But is this a sensible MSD? As the values given in a >>>>>>> paper i was referring was in Ang^2 >>>>>>> J. Chem. Theory Comput. 2012, 8, 1129-1142 >>>>>>> >>>>>>> >>>>>>> Command that i used - >>>>>>> >>>>>>> echo 3 3 |g_msd -f a.xtc -s a.tpr -o a.xvg -n a.ndx -trestart 10 -b >>>>>>> 4000 >>>>>>> -e 50000 -rmcomm >>>>>>> >>>>>>> Is the range of diffusion coefficient of proteins of in water l >>>>>>> in the range of x e-5 cm^2/s? (hemoglobin is 0.1 e-5 cm^2/s) >>>>>>> >>>>>>> Thank you >>>>>>> kavya >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> >>>>>> ==============================******========== >>>>> >>>>> >>>>> >>>>> 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**< >>>>> http://vt.edu/Pages/Personal/**justin<http://vt.edu/Pages/Personal/justin> >>>>> > >>>>> <h**ttp://www.bevanlab.**biochem.vt.**edu/Pages/**Personal/justin< >>>>> http://www.**bevanlab.biochem.vt.edu/Pages/**Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> >>>>> > >>>>> >>>>>> >>>>>> >>>>> ==============================******========== >>>>> >>>>> >>>>> -- >>>>> gmx-users mailing list gmx-users@gromacs.org >>>>> http://lists.gromacs.org/******mailman/listinfo/gmx-users<http://lists.gromacs.org/****mailman/listinfo/gmx-users> >>>>> <htt**p://lists.gromacs.org/****mailman/listinfo/gmx-users<http://lists.gromacs.org/**mailman/listinfo/gmx-users> >>>>> > >>>>> <htt**p://lists.gromacs.org/**mailman/**listinfo/gmx-users<http://lists.gromacs.org/mailman/**listinfo/gmx-users> >>>>> <h**ttp://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >>>>> > >>>>> >>>>> >>>>>> * Please search the archive at http://www.gromacs.org/** >>>>> Support/Mailing_Lists/Search<**h**ttp://www.gromacs.org/**Support/**<http://www.gromacs.org/Support/**> >>>>> >>>>> Mailing_Lists/Search<http://**www.gromacs.org/Support/** >>>>> Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search> >>>>> >>before >>>>> posting! >>>>> >>>>> * Please don't post (un)subscribe requests to the list. Use the www >>>>> interface or send it to gmx-users-requ...@gromacs.org. >>>>> * Can't post? Read >>>>> http://www.gromacs.org/******Support/Mailing_Lists<http://www.gromacs.org/****Support/Mailing_Lists> >>>>> <http://**www.gromacs.org/**Support/**Mailing_Lists<http://www.gromacs.org/**Support/Mailing_Lists> >>>>> > >>>>> <http://**www.gromacs.org/**Support/**Mailing_Lists<http://www.gromacs.org/Support/**Mailing_Lists> >>>>> <http:/**/www.gromacs.org/Support/**Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >>>>> > >>>>> >>>>>> >>>>>> >>>>> >>>>> -- >>> ==============================****========== >>> >>> 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<http://vt.edu/Pages/Personal/justin> >>> <h**ttp://www.bevanlab.biochem.vt.**edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> >>> > >>> >>> ==============================****========== >>> -- >>> gmx-users mailing list gmx-users@gromacs.org >>> http://lists.gromacs.org/****mailman/listinfo/gmx-users<http://lists.gromacs.org/**mailman/listinfo/gmx-users> >>> <htt**p://lists.gromacs.org/mailman/**listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >>> > >>> * Please search the archive at http://www.gromacs.org/** >>> Support/Mailing_Lists/Search<h**ttp://www.gromacs.org/Support/** >>> Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>>before >>> posting! >>> * Please don't post (un)subscribe requests to the list. 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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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > * Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? 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