Re: [gmx-users] Regarding RMSD analysis result
Hi Ahmet, What exactly is the RMSD? Well, it's the average distance between corresponding particles in two structures. So, an RMSD of 2 nm means that, on average, each particle moved by 2 nm. How large is your protein at the start? How likely is it that you have such differences on average, after superposition? You can also look at it in a different way. The RMSD between two structures is the difference between the radii of gyration and the 'correspondence'; think of distance: (a-b)^2 = a^2 + b^2 - 2ab. Thus, the upper limit of the RMSD by definition is equal to the sum of the radii of gyration. Those shouldn't change too much from the crystal structure, so you can make an estimate of what you can expect based on that. Of course, you'll only get the upper bound if there is no correspondence whatsoever. For a protein, that is impossible, because of the order and spatial correlation imposed by the bonds. Hope it clarifies a bit... Cheers, Tsjerk On Tue, Sep 25, 2012 at 7:10 AM, ahmet yıldırım ahmedo...@gmail.com wrote: Dear Tsjerk, You said RMSD's above 1 nm are suspect, towards 2 highly likely not correct. What is the physical/biological/chemical meaning of what you say? Greetings 2012/9/24 Tsjerk Wassenaar tsje...@gmail.com Hi, RMSD's above 1 nm are suspect, towards 2 highly likely not correct. You have to make sure that the molecule is made whole before doing RMSD analysis. Cheers, Tsjerk On Mon, Sep 24, 2012 at 3:02 PM, lloyd riggs lloyd.ri...@gmx.ch wrote: You can also just quickly visualize it in VMD and see if anything your looking at is not centred properly. If it isnt you just have to centre it. Stephan Original-Nachricht Datum: Mon, 24 Sep 2012 04:32:33 -0700 Von: naga sundar naga25sun...@gmail.com An: Discussion list for GROMACS users gmx-users@gromacs.org Betreff: Re: [gmx-users] Regarding RMSD analysis result Dear justin Thanks for ur suggestions While speaking about periodic conditions, I followed the similar condition for both native and mutant complexes. For native complexes not any big deviation was observed. So its confirmed that nothing wrong with periodic conditions. Since all the three mutations were having high clinical significance, we assuming mutation is the only reason for this abnormal RMSD behavior. Sudden big increase in the RMSD was observed in previous mutational MD studies. http://www.sciencedirect.com/science/article/pii/S0006291X08020792. Overall, all the factors are supporting our results. So shall we take this RMSD analysis as good result . Even after repeating the 20 ns MD simulation two times i got the same results. On Mon, Sep 24, 2012 at 3:41 AM, Justin Lemkul jalem...@vt.edu wrote: On 9/24/12 6:24 AM, naga sundar wrote: Dear gromacs users We performed MD simulation analysis for native and mutant models of protein-protein complexes. From 20 ns simulation trajectory, we generated RMSD graph for one native and three mutant complexes. For native complex in the entire simulation period, we observed a constant RMSD (~0.15 to ~ 0.25 nm). But, three mutant complexes showed drastic fluctuation in theRMSD (~0.15 to ~1.75) plot. We analysed all the 3D structure's in the fluctuated areas observed destruction of protein complexes. All the three mutants were already experimentally analyzed and reported that they are involved in the destruction of protein-protein interactions. Query 1: What may be the reason for sudden rise and fall of the RMSD values in mutant complexes. We are assume its because of the involvement of mutation. Query 2: Is there may any other reasons for drastic fluctuation in the RMSD Query 3: Observed results are rite. Here iam attaching the RMSD graph for your observation. Attachments to the list do not work. You will have to post a link to a file sharing site if you wish to share an image. Such jumps in RMSD are very suspect. Since you are dealing with protein-protein complexes, accounting for periodicity can be very challenging. Have you properly fit the trajectory such that your protein subunits are not jumping across periodic boundaries? If they are, then your results are nothing more than an artifact. If they are not, then you have something more interesting, but a tenfold increase in RMSD is very peculiar. -Justin -- ==**== 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://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx
Re: [gmx-users] Regarding RMSD analysis result
Dear justin
http://rmsdnagasundaram.blogspot.in/. This is the link to
my rmsd graph. Plz check it once and suggest me.
Thanks
On Mon, Sep 24, 2012 at 10:10 PM, ahmet yıldırım ahmedo...@gmail.comwrote:
Dear Tsjerk,
You said RMSD's above 1 nm are suspect, towards 2 highly likely not
correct. What is the physical/biological/chemical meaning of what you say?
Greetings
2012/9/24 Tsjerk Wassenaar tsje...@gmail.com
Hi,
RMSD's above 1 nm are suspect, towards 2 highly likely not correct.
You have to make sure that the molecule is made whole before doing
RMSD analysis.
Cheers,
Tsjerk
On Mon, Sep 24, 2012 at 3:02 PM, lloyd riggs lloyd.ri...@gmx.ch wrote:
You can also just quickly visualize it in VMD and see if anything your
looking at is not centred properly. If it isnt you just have to centre
it.
Stephan
Original-Nachricht
Datum: Mon, 24 Sep 2012 04:32:33 -0700
Von: naga sundar naga25sun...@gmail.com
An: Discussion list for GROMACS users gmx-users@gromacs.org
Betreff: Re: [gmx-users] Regarding RMSD analysis result
Dear justin
Thanks for ur suggestions
While speaking about periodic conditions, I
followed
the similar condition for both native and mutant complexes. For native
complexes not any big deviation was observed. So its confirmed that
nothing
wrong with periodic conditions. Since all the three mutations were
having
high clinical significance, we assuming mutation is the only reason
for
this abnormal RMSD behavior. Sudden big increase in the RMSD was
observed
in previous mutational MD studies.
http://www.sciencedirect.com/science/article/pii/S0006291X08020792.
Overall, all the factors are supporting our results. So shall we take
this
RMSD analysis as good result . Even after repeating the 20 ns MD
simulation
two times i got the same results.
On Mon, Sep 24, 2012 at 3:41 AM, Justin Lemkul jalem...@vt.edu
wrote:
On 9/24/12 6:24 AM, naga sundar wrote:
Dear gromacs users
We performed MD simulation analysis for native and
mutant
models of protein-protein complexes. From 20 ns simulation
trajectory,
we
generated RMSD graph for one native and three mutant complexes. For
native
complex in the entire simulation period, we observed a constant
RMSD
(~0.15 to ~ 0.25 nm). But, three mutant complexes
showed drastic fluctuation in theRMSD (~0.15 to ~1.75) plot. We
analysed
all the 3D structure's in the fluctuated areas observed destruction
of
protein complexes.
All the three mutants were already experimentally analyzed and
reported
that they are involved in the destruction of protein-protein
interactions.
Query 1: What may be the reason for sudden rise and fall of the
RMSD
values
in mutant complexes. We are assume its because of the involvement
of
mutation.
Query 2: Is there may any other reasons for drastic fluctuation in
the
RMSD
Query 3: Observed results are rite.
Here iam attaching the RMSD graph for your observation.
Attachments to the list do not work. You will have to post a link
to
a
file sharing site if you wish to share an image.
Such jumps in RMSD are very suspect. Since you are dealing with
protein-protein complexes, accounting for periodicity can be very
challenging. Have you properly fit the trajectory such that your
protein
subunits are not jumping across periodic boundaries? If they are,
then
your results are nothing more than an artifact. If they are not,
then
you
have something more interesting, but a tenfold increase in RMSD is
very
peculiar.
-Justin
--
==**==
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://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
==**==
--
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Regards
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--
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Re: [gmx-users] Regarding RMSD analysis result
It looks for me like the known pbc effect others already pointed to. If you have just a protein-ligand complex (+ water and counterions of course) it's relatively easy to manually (a piece of code would do it) bring the ligand to the correct position in the frames showing an abnormally high value by subtracting half the x/y dimension of the box from its coordinates and re-calculate the rmsd , but I think trjconv would do it as well. Felipe On 09/25/2012 09:22 AM, naga sundar wrote: Dear justin http://rmsdnagasundaram.blogspot.in/. This is the link to my rmsd graph. Plz check it once and suggest me. Thanks -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at 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
Re: [gmx-users] Regarding RMSD analysis result
Dear Felipe Thanks for ur reply. The system is a protein-protein complex. Like u r saying its due to pbc problem then why any abnormality doesn't happened to the native complex (Black line)?. As already suggest by justin i checked the pbc conditions upto my knowledge everything is fine. of-course this is not the first MD run for these native and mutant complexes. I run twice and got the same results. I want know this kind of RMSD is rite r wrong?.. On Tue, Sep 25, 2012 at 12:45 AM, Felipe Pineda, PhD luis.pinedadecas...@lnu.se wrote: It looks for me like the known pbc effect others already pointed to. If you have just a protein-ligand complex (+ water and counterions of course) it's relatively easy to manually (a piece of code would do it) bring the ligand to the correct position in the frames showing an abnormally high value by subtracting half the x/y dimension of the box from its coordinates and re-calculate the rmsd , but I think trjconv would do it as well. Felipe On 09/25/2012 09:22 AM, naga sundar wrote: Dear justin http://rmsdnagasundaram.**blogspot.in/http://rmsdnagasundaram.blogspot.in/. This is the link to my rmsd graph. Plz check it once and suggest me. Thanks -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Regards N.NagaSundaram -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at 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
Re: [gmx-users] Regarding RMSD analysis result
On 09/25/2012 10:08 AM, naga sundar wrote: Dear Felipe Thanks for ur reply. The system is a protein-protein complex. Like u r saying its due to pbc problem then why any abnormality doesn't happened to the native complex (Black line)?. Maybe because MD is stochastic ... As already suggest by justin i checked the pbc conditions upto my knowledge everything is fine. As Justin said, it's not about the pbc conditions as they appear in the mdp file, but about pbc effects due to a chain, probably the ligand, leaving the box and being reflected to the opposite side. Have you checked out visually how the weird frames look like? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at 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
Re: [gmx-users] Regarding RMSD analysis result
Hi, Your RMSD graph is ok but is represented wrong due to pbc problem. Use whole and nojump options of trjconv. On Tue, Sep 25, 2012 at 2:15 PM, Felipe Pineda, PhD luis.pinedadecas...@lnu.se wrote: On 09/25/2012 10:08 AM, naga sundar wrote: Dear Felipe Thanks for ur reply. The system is a protein-protein complex. Like u r saying its due to pbc problem then why any abnormality doesn't happened to the native complex (Black line)?. Maybe because MD is stochastic ... As already suggest by justin i checked the pbc conditions upto my knowledge everything is fine. As Justin said, it's not about the pbc conditions as they appear in the mdp file, but about pbc effects due to a chain, probably the ligand, leaving the box and being reflected to the opposite side. Have you checked out visually how the weird frames look like? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at 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
Re: [gmx-users] Regarding RMSD analysis result
Hi, trjconv -s top.tpr -f traj.xtc -o traj-nojump.xtc -pbc nojump I hope it helps 2012/9/25 Archana Sonawani ask.arch...@gmail.com Hi, Your RMSD graph is ok but is represented wrong due to pbc problem. Use whole and nojump options of trjconv. On Tue, Sep 25, 2012 at 2:15 PM, Felipe Pineda, PhD luis.pinedadecas...@lnu.se wrote: On 09/25/2012 10:08 AM, naga sundar wrote: Dear Felipe Thanks for ur reply. The system is a protein-protein complex. Like u r saying its due to pbc problem then why any abnormality doesn't happened to the native complex (Black line)?. Maybe because MD is stochastic ... As already suggest by justin i checked the pbc conditions upto my knowledge everything is fine. As Justin said, it's not about the pbc conditions as they appear in the mdp file, but about pbc effects due to a chain, probably the ligand, leaving the box and being reflected to the opposite side. Have you checked out visually how the weird frames look like? -- gmx-users mailing listgmx-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/Searchbefore 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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at 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 -- Ahmet Yıldırım -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at 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
Re: [gmx-users] Regarding RMSD analysis result
On 9/24/12 6:24 AM, naga sundar wrote: Dear gromacs users We performed MD simulation analysis for native and mutant models of protein-protein complexes. From 20 ns simulation trajectory, we generated RMSD graph for one native and three mutant complexes. For native complex in the entire simulation period, we observed a constant RMSD (~0.15 to ~ 0.25 nm). But, three mutant complexes showed drastic fluctuation in theRMSD (~0.15 to ~1.75) plot. We analysed all the 3D structure's in the fluctuated areas observed destruction of protein complexes. All the three mutants were already experimentally analyzed and reported that they are involved in the destruction of protein-protein interactions. Query 1: What may be the reason for sudden rise and fall of the RMSD values in mutant complexes. We are assume its because of the involvement of mutation. Query 2: Is there may any other reasons for drastic fluctuation in the RMSD Query 3: Observed results are rite. Here iam attaching the RMSD graph for your observation. Attachments to the list do not work. You will have to post a link to a file sharing site if you wish to share an image. Such jumps in RMSD are very suspect. Since you are dealing with protein-protein complexes, accounting for periodicity can be very challenging. Have you properly fit the trajectory such that your protein subunits are not jumping across periodic boundaries? If they are, then your results are nothing more than an artifact. If they are not, then you have something more interesting, but a tenfold increase in RMSD is very peculiar. -Justin -- 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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at 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
Re: [gmx-users] Regarding RMSD analysis result
Dear justin Thanks for ur suggestions While speaking about periodic conditions, I followed the similar condition for both native and mutant complexes. For native complexes not any big deviation was observed. So its confirmed that nothing wrong with periodic conditions. Since all the three mutations were having high clinical significance, we assuming mutation is the only reason for this abnormal RMSD behavior. Sudden big increase in the RMSD was observed in previous mutational MD studies. http://www.sciencedirect.com/science/article/pii/S0006291X08020792. Overall, all the factors are supporting our results. So shall we take this RMSD analysis as good result . Even after repeating the 20 ns MD simulation two times i got the same results. On Mon, Sep 24, 2012 at 3:41 AM, Justin Lemkul jalem...@vt.edu wrote: On 9/24/12 6:24 AM, naga sundar wrote: Dear gromacs users We performed MD simulation analysis for native and mutant models of protein-protein complexes. From 20 ns simulation trajectory, we generated RMSD graph for one native and three mutant complexes. For native complex in the entire simulation period, we observed a constant RMSD (~0.15 to ~ 0.25 nm). But, three mutant complexes showed drastic fluctuation in theRMSD (~0.15 to ~1.75) plot. We analysed all the 3D structure's in the fluctuated areas observed destruction of protein complexes. All the three mutants were already experimentally analyzed and reported that they are involved in the destruction of protein-protein interactions. Query 1: What may be the reason for sudden rise and fall of the RMSD values in mutant complexes. We are assume its because of the involvement of mutation. Query 2: Is there may any other reasons for drastic fluctuation in the RMSD Query 3: Observed results are rite. Here iam attaching the RMSD graph for your observation. Attachments to the list do not work. You will have to post a link to a file sharing site if you wish to share an image. Such jumps in RMSD are very suspect. Since you are dealing with protein-protein complexes, accounting for periodicity can be very challenging. Have you properly fit the trajectory such that your protein subunits are not jumping across periodic boundaries? If they are, then your results are nothing more than an artifact. If they are not, then you have something more interesting, but a tenfold increase in RMSD is very peculiar. -Justin -- ==**== 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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Regards N.NagaSundaram -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at 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
Re: [gmx-users] Regarding RMSD analysis result
On 9/24/12 7:32 AM, naga sundar wrote: Dear justin Thanks for ur suggestions While speaking about periodic conditions, I followed the similar condition for both native and mutant complexes. For native complexes not any big deviation was observed. So its confirmed that nothing wrong with periodic conditions. Since all the three mutations were having I think you may have misunderstood what I was saying. I was not referring to the simulation conditions themselves, but rather the normal post-processing of the trajectory with trjconv to assure a continuous image of the trajectory. If one subunit crosses a periodic boundary (as a consequence of normal diffusion), you will see a sudden spike in the RMSD value. You must correct for this effect using trjconv before running analysis. http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions#Suggested_trjconv_workflow high clinical significance, we assuming mutation is the only reason for this abnormal RMSD behavior. Sudden big increase in the RMSD was observed in previous mutational MD studies. http://www.sciencedirect.com/science/article/pii/S0006291X08020792. Overall, all the factors are supporting our results. So shall we take this RMSD analysis as good result . Even after repeating the 20 ns MD simulation two times i got the same results. Without seeing any evidence from your work, I would not be prepared to agree with your conclusions. -Justin -- 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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at 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
Re: [gmx-users] Regarding RMSD analysis result
You can also just quickly visualize it in VMD and see if anything your looking at is not centred properly. If it isnt you just have to centre it. Stephan Original-Nachricht Datum: Mon, 24 Sep 2012 04:32:33 -0700 Von: naga sundar naga25sun...@gmail.com An: Discussion list for GROMACS users gmx-users@gromacs.org Betreff: Re: [gmx-users] Regarding RMSD analysis result Dear justin Thanks for ur suggestions While speaking about periodic conditions, I followed the similar condition for both native and mutant complexes. For native complexes not any big deviation was observed. So its confirmed that nothing wrong with periodic conditions. Since all the three mutations were having high clinical significance, we assuming mutation is the only reason for this abnormal RMSD behavior. Sudden big increase in the RMSD was observed in previous mutational MD studies. http://www.sciencedirect.com/science/article/pii/S0006291X08020792. Overall, all the factors are supporting our results. So shall we take this RMSD analysis as good result . Even after repeating the 20 ns MD simulation two times i got the same results. On Mon, Sep 24, 2012 at 3:41 AM, Justin Lemkul jalem...@vt.edu wrote: On 9/24/12 6:24 AM, naga sundar wrote: Dear gromacs users We performed MD simulation analysis for native and mutant models of protein-protein complexes. From 20 ns simulation trajectory, we generated RMSD graph for one native and three mutant complexes. For native complex in the entire simulation period, we observed a constant RMSD (~0.15 to ~ 0.25 nm). But, three mutant complexes showed drastic fluctuation in theRMSD (~0.15 to ~1.75) plot. We analysed all the 3D structure's in the fluctuated areas observed destruction of protein complexes. All the three mutants were already experimentally analyzed and reported that they are involved in the destruction of protein-protein interactions. Query 1: What may be the reason for sudden rise and fall of the RMSD values in mutant complexes. We are assume its because of the involvement of mutation. Query 2: Is there may any other reasons for drastic fluctuation in the RMSD Query 3: Observed results are rite. Here iam attaching the RMSD graph for your observation. Attachments to the list do not work. You will have to post a link to a file sharing site if you wish to share an image. Such jumps in RMSD are very suspect. Since you are dealing with protein-protein complexes, accounting for periodicity can be very challenging. Have you properly fit the trajectory such that your protein subunits are not jumping across periodic boundaries? If they are, then your results are nothing more than an artifact. If they are not, then you have something more interesting, but a tenfold increase in RMSD is very peculiar. -Justin -- ==**== 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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Regards N.NagaSundaram -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at 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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at 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
Re: [gmx-users] Regarding RMSD analysis result
Hi, RMSD's above 1 nm are suspect, towards 2 highly likely not correct. You have to make sure that the molecule is made whole before doing RMSD analysis. Cheers, Tsjerk On Mon, Sep 24, 2012 at 3:02 PM, lloyd riggs lloyd.ri...@gmx.ch wrote: You can also just quickly visualize it in VMD and see if anything your looking at is not centred properly. If it isnt you just have to centre it. Stephan Original-Nachricht Datum: Mon, 24 Sep 2012 04:32:33 -0700 Von: naga sundar naga25sun...@gmail.com An: Discussion list for GROMACS users gmx-users@gromacs.org Betreff: Re: [gmx-users] Regarding RMSD analysis result Dear justin Thanks for ur suggestions While speaking about periodic conditions, I followed the similar condition for both native and mutant complexes. For native complexes not any big deviation was observed. So its confirmed that nothing wrong with periodic conditions. Since all the three mutations were having high clinical significance, we assuming mutation is the only reason for this abnormal RMSD behavior. Sudden big increase in the RMSD was observed in previous mutational MD studies. http://www.sciencedirect.com/science/article/pii/S0006291X08020792. Overall, all the factors are supporting our results. So shall we take this RMSD analysis as good result . Even after repeating the 20 ns MD simulation two times i got the same results. On Mon, Sep 24, 2012 at 3:41 AM, Justin Lemkul jalem...@vt.edu wrote: On 9/24/12 6:24 AM, naga sundar wrote: Dear gromacs users We performed MD simulation analysis for native and mutant models of protein-protein complexes. From 20 ns simulation trajectory, we generated RMSD graph for one native and three mutant complexes. For native complex in the entire simulation period, we observed a constant RMSD (~0.15 to ~ 0.25 nm). But, three mutant complexes showed drastic fluctuation in theRMSD (~0.15 to ~1.75) plot. We analysed all the 3D structure's in the fluctuated areas observed destruction of protein complexes. All the three mutants were already experimentally analyzed and reported that they are involved in the destruction of protein-protein interactions. Query 1: What may be the reason for sudden rise and fall of the RMSD values in mutant complexes. We are assume its because of the involvement of mutation. Query 2: Is there may any other reasons for drastic fluctuation in the RMSD Query 3: Observed results are rite. Here iam attaching the RMSD graph for your observation. Attachments to the list do not work. You will have to post a link to a file sharing site if you wish to share an image. Such jumps in RMSD are very suspect. Since you are dealing with protein-protein complexes, accounting for periodicity can be very challenging. Have you properly fit the trajectory such that your protein subunits are not jumping across periodic boundaries? If they are, then your results are nothing more than an artifact. If they are not, then you have something more interesting, but a tenfold increase in RMSD is very peculiar. -Justin -- ==**== 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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Regards N.NagaSundaram -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at 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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at 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 -- Tsjerk A. Wassenaar
Re: [gmx-users] Regarding RMSD analysis result
Dear Tsjerk, You said RMSD's above 1 nm are suspect, towards 2 highly likely not correct. What is the physical/biological/chemical meaning of what you say? Greetings 2012/9/24 Tsjerk Wassenaar tsje...@gmail.com Hi, RMSD's above 1 nm are suspect, towards 2 highly likely not correct. You have to make sure that the molecule is made whole before doing RMSD analysis. Cheers, Tsjerk On Mon, Sep 24, 2012 at 3:02 PM, lloyd riggs lloyd.ri...@gmx.ch wrote: You can also just quickly visualize it in VMD and see if anything your looking at is not centred properly. If it isnt you just have to centre it. Stephan Original-Nachricht Datum: Mon, 24 Sep 2012 04:32:33 -0700 Von: naga sundar naga25sun...@gmail.com An: Discussion list for GROMACS users gmx-users@gromacs.org Betreff: Re: [gmx-users] Regarding RMSD analysis result Dear justin Thanks for ur suggestions While speaking about periodic conditions, I followed the similar condition for both native and mutant complexes. For native complexes not any big deviation was observed. So its confirmed that nothing wrong with periodic conditions. Since all the three mutations were having high clinical significance, we assuming mutation is the only reason for this abnormal RMSD behavior. Sudden big increase in the RMSD was observed in previous mutational MD studies. http://www.sciencedirect.com/science/article/pii/S0006291X08020792. Overall, all the factors are supporting our results. So shall we take this RMSD analysis as good result . Even after repeating the 20 ns MD simulation two times i got the same results. On Mon, Sep 24, 2012 at 3:41 AM, Justin Lemkul jalem...@vt.edu wrote: On 9/24/12 6:24 AM, naga sundar wrote: Dear gromacs users We performed MD simulation analysis for native and mutant models of protein-protein complexes. From 20 ns simulation trajectory, we generated RMSD graph for one native and three mutant complexes. For native complex in the entire simulation period, we observed a constant RMSD (~0.15 to ~ 0.25 nm). But, three mutant complexes showed drastic fluctuation in theRMSD (~0.15 to ~1.75) plot. We analysed all the 3D structure's in the fluctuated areas observed destruction of protein complexes. All the three mutants were already experimentally analyzed and reported that they are involved in the destruction of protein-protein interactions. Query 1: What may be the reason for sudden rise and fall of the RMSD values in mutant complexes. We are assume its because of the involvement of mutation. Query 2: Is there may any other reasons for drastic fluctuation in the RMSD Query 3: Observed results are rite. Here iam attaching the RMSD graph for your observation. Attachments to the list do not work. You will have to post a link to a file sharing site if you wish to share an image. Such jumps in RMSD are very suspect. Since you are dealing with protein-protein complexes, accounting for periodicity can be very challenging. Have you properly fit the trajectory such that your protein subunits are not jumping across periodic boundaries? If they are, then your results are nothing more than an artifact. If they are not, then you have something more interesting, but a tenfold increase in RMSD is very peculiar. -Justin -- ==**== 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://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-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/Searchbefore 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 -- Regards N.NagaSundaram -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at 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 -- gmx-users mailing listgmx-users@gromacs.org
