[gmx-users] mixing of PCs for generating reduced free energy profile using g_sham
Hi Gromacs user community a) I was wondering if it is possible to mix a common pair of PCs from two simulations (say, PC1 from a bound simulation vs PC1 from unbound simulation or for that matter wild vs mutant) as an reaction coordinates to generate a comparative reduced free energy profile using the g_sham utility. b) Will such a approach generate a meaningful comparative free energy plot, akin to an conformational landscape plot commonly generated by plotting PC1 of one system vs. PC1 another system, to highlight the difference /overlap in the conformational sub-space sampled by the two systems c) Given my understanding of underlying formula ∆G(R) = -*KBT *[ln P(R) – ln P(max)] as implemented in g_sham i presume that it is impossible, since mixing of PCs from two different systems will not ensure a proper probability distribution, the data points has to be similar. Thanking in advance Regards, Vijayan.R -- 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] Re: Attention:urgent
Plz be very specific about your problem. In fact iam not able to find out that problem is. what is the error msg what did you do do you need a sge script to submit job in a super computer or a cluster??? if so then what queing system all thes ethings are very imp On Thu, Jul 26, 2012 at 7:33 AM, Mark Abraham mark.abra...@anu.edu.au wrote: On 26/07/2012 9:21 PM, Arunima Kumar wrote: Dear Sir I am Arunima Kumar Verma..a researcher from India. I found your email id from mailing list mentioned in GROMACS. Then you will have seen there the frequent requests from people not to make personal requests for help on general GROMACS topics. I need your urgent help. Actually i have been striving hard to solve the problems i am facing in molecular dynamics simulation of my protein. Your need is urgent to me when you're paying me ;-) Being from pure biological sciences background and qulaified CSIR-NET...i am more acquainted with life sciences. Though i have done my PG in bioinformatic yet i have problems in computational aspects. Sir, presently i have put my protein molecule to simulation by GROMACS and facing problems while running grompp or mdrun commands. I earnestly request if you can help in creating SGE script for the same. I would be highly obliged sir. Plz help You should start by doing all the tutorial material you can find with Google, even if you don't think the tutorial topic is particularly relevant, and reading as widely as possible, particularly including the manual. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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 * Only plain text messages are allowed! * 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] RIMSP calculation
Hi Gromacs users I am trying to measure the similarity of the subspace sampled by a mutant protein-Ligand complex versus a wild type complex based on the eigen vectors computed using PCA. I was wondering, does and handy scripts does exists to compute the root mean square inner product ( RMSIP). It would be really thankful if any one could provide me a script for RMSIP calculation or kindly let me know if there exists any way to compute RMSIP directly using Gromacs. My second question is ( sorry as this is a general question) I have come across many papers where they employ RMSIP to quantify the similarity between PC1 and PC2 derived by essential dynamics and in turn use the values to prove the convergence of conformational sampling. Is this a well settled proposition to drive home the point that the simulation has converged or should i compute the cosine content to prove the same. Which of this is a superior metric ? Thanking in advance Regards Vijayan.R -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] RIMSP calculation
Hi Tsjerk Many thanks for your kind response. Got the script, will try to run it. Also thanks for clarifying RMSIP vs Cosine content values. Regards Vijayan.R On Thu, Jun 28, 2012 at 10:56 AM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Vijayan, There must be a script somewhere in the archives (http://www.mail-archive.com/gmx-users@gromacs.org/msg02871.html) that calculates the RMSIP from the XPM file of eigenvector inner products. I have come across many papers where they employ RMSIP to quantify the similarity between PC1 and PC2 derived by essential dynamics and in turn use the values to prove the convergence of conformational sampling. Is this a well settled proposition to drive home the point that the simulation has converged or should i compute the cosine content to prove the same. Which of this is a superior metric ? The RMSIP only indicates whether the subspaces sampled are similar, nothing about the extent of sampling, and nothing about the convergence. The essential subspace (ugh, ugh, cough!, pardon me) usually converges much faster than the sampling. And the cosine content... Well, it will show you whether the simulation did not yet converge. Check some recent replies I gave on the list about that. Cheers, Tsjerk Thanking in advance Regards Vijayan.R -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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 * Only plain text messages are allowed! * 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] constraints between protein ligand - metal chelation
Many thanks for your response On Mon, May 21, 2012 at 12:01 PM, francesco oteri francesco.ot...@gmail.com wrote: You are right Peter 2012/5/21 Peter C. Lai p...@uab.edu This approach still requires the system to be parameterized as a single moleculetype, doesn't it? On 2012-05-20 04:42:26PM +0200, francesco oteri wrote: Hi, if you are able to define atom couples able to mantein the structure of your complex, you can insert in .top file a set of bond using function 6 (see table at pag 125 of the user manual). For example, let atom 1 and 100 are at distance 0.6nm, you can insert in .top a row like 1 100 6 0.6 1000 you impose a bond between the two atoms having as eauilibrium distance 0.6nm and force strenght 1000J. Function 6 doesn't implie the generation of angles and dihedrals so it is the right choice to impose distance restraints Francesco 2012/5/20 R.S.K.Vijayan biovija...@gmail.com Many thanks for your response. No special reasons for parametrizing the ligand and the protein as a separate system. I dont think that the ligand and protein can be parametrized as a single system, but will definitely try doing it as a single system and see if it works. Regards Vijayan.R On Sat, May 19, 2012 at 10:23 PM, Peter C. Lai p...@uab.edu wrote: Is there a particular reason why the ligand has been parameterized as a separate moleculetype from the protein in your case? I prefer to treat coordination bonds as real bonds instead of relying on electrostatic interactions anyway, since it is the only way to conservatively ensure the coordination geometry is preserved (like for Zn, where QM predicts a tetrahedral geometry but Zn free ions will result in an octahedral geometry). In any case, even if you stick with freeion Zn, you can paramaterize the complex as a single moleculetype and use distance restraints there, can't you? On 2012-05-19 09:42:25PM -0400, R.S.K.Vijayan wrote: Dear Gromacs users I was wondering if there exists any technique that sets distance restraint between specified ligand (atoms) and the protein(atoms) in Gromacs. I am simulating a system which contains metal ions coordinated to the Ligand. I looked in to the mailing list and Gromacs manual and figured out that *genrster* can be employed, to set distance, position and dihedral restraints. Unfortunately i also stumbled on the fact that restraints between systems is not possible. Since force fields are not good at handling chelation between metal atoms, i find that the metals drifting away from the coordinated ligand atoms during the course of simulation, hence i introduced position constraints for the metal and ended up realizing that the coordination distance between the ligand and the metal exceeds the permissible range and the angles between the chelating atoms gets distorted and some coordinating residues like Histidine and Aspartic acid also moves away from the metal. Hence, i was wondering if l anyone knows of any method (apart from QM/MM) that can help to set distance restraints between the protein (metal ion ) and the ligand, also any suggestion that could help in handling ligand metal chelation is welcomed. Thanking in advance Regards Vijayan.R -- 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 -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808| == -- 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
[gmx-users] constraints between protein ligand - metal chelation
Dear Gromacs users I was wondering if there exists any technique that sets distance restraint between specified ligand (atoms) and the protein(atoms) in Gromacs. I am simulating a system which contains metal ions coordinated to the Ligand. I looked in to the mailing list and Gromacs manual and figured out that *genrster* can be employed, to set distance, position and dihedral restraints. Unfortunately i also stumbled on the fact that restraints between systems is not possible. Since force fields are not good at handling chelation between metal atoms, i find that the metals drifting away from the coordinated ligand atoms during the course of simulation, hence i introduced position constraints for the metal and ended up realizing that the coordination distance between the ligand and the metal exceeds the permissible range and the angles between the chelating atoms gets distorted and some coordinating residues like Histidine and Aspartic acid also moves away from the metal. Hence, i was wondering if l anyone knows of any method (apart from QM/MM) that can help to set distance restraints between the protein (metal ion ) and the ligand, also any suggestion that could help in handling ligand metal chelation is welcomed. Thanking in advance Regards Vijayan.R -- 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] constraints between protein ligand - metal chelation
Many thanks for your response. No special reasons for parametrizing the ligand and the protein as a separate system. I dont think that the ligand and protein can be parametrized as a single system, but will definitely try doing it as a single system and see if it works. Regards Vijayan.R On Sat, May 19, 2012 at 10:23 PM, Peter C. Lai p...@uab.edu wrote: Is there a particular reason why the ligand has been parameterized as a separate moleculetype from the protein in your case? I prefer to treat coordination bonds as real bonds instead of relying on electrostatic interactions anyway, since it is the only way to conservatively ensure the coordination geometry is preserved (like for Zn, where QM predicts a tetrahedral geometry but Zn free ions will result in an octahedral geometry). In any case, even if you stick with freeion Zn, you can paramaterize the complex as a single moleculetype and use distance restraints there, can't you? On 2012-05-19 09:42:25PM -0400, R.S.K.Vijayan wrote: Dear Gromacs users I was wondering if there exists any technique that sets distance restraint between specified ligand (atoms) and the protein(atoms) in Gromacs. I am simulating a system which contains metal ions coordinated to the Ligand. I looked in to the mailing list and Gromacs manual and figured out that *genrster* can be employed, to set distance, position and dihedral restraints. Unfortunately i also stumbled on the fact that restraints between systems is not possible. Since force fields are not good at handling chelation between metal atoms, i find that the metals drifting away from the coordinated ligand atoms during the course of simulation, hence i introduced position constraints for the metal and ended up realizing that the coordination distance between the ligand and the metal exceeds the permissible range and the angles between the chelating atoms gets distorted and some coordinating residues like Histidine and Aspartic acid also moves away from the metal. Hence, i was wondering if l anyone knows of any method (apart from QM/MM) that can help to set distance restraints between the protein (metal ion ) and the ligand, also any suggestion that could help in handling ligand metal chelation is welcomed. Thanking in advance Regards Vijayan.R -- 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 -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808| == -- 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
[gmx-users] query about identifying representative snapshots from a 2D FEL
Dear Gromacs users I am interested in identifying the representative snapshots from a 2D Free energy landscape plot generated using g_sham using the reaction coordinates obtained from EV1 and EV2 projections. Can some suggest on how to back trace the coordinates from a 2D FEL and also the time. To be more precise i want to carry out an analysis exactly like what has been reported in Figure 8 of this refereed paper http://pubs.rsc.org/en/content/articlehtml/2011/cp/c0cp02697b Your suggestions would be greatly appreciated Thanking you in advance Regards Vijayan.R -- 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] Simulating multiple fragments
Hi all I was wondering if some body has done simulating multiple copies of small lead like fragments in a solvated box . I want to soak my proteins with multiple copies of diverse fragments along with water as iam interested in finding the hot spots in proteins that can be successfully employed for fragment based drug design. The approach is analogs to the MCSS approach developed by Prof Karplus and the recent SILCS approach by Prof Mackerell. The impediments which i theoretically fore see are 1) how to negate interactions terms between two fragments as two fragments may be competing for the same site. 2) How to create multiple topologies for multiple copies of the same fragment randomly placed all over the fragment 3) Iam also skeptical whether the fragments will be able to find their respective binding site in a nanosecond time scale when started De Novo contrary to the well settled proposition of docking and keeping the fragment in the active site. A look at this paper by DE Shaw How Does a Drug Molecule Find Its Target Binding Site?? reveals the binding event to be captured on a mili second time second. Thanking you in advance for all thought provoking suggestions. Regards Vijayan.R On Sat, Jan 14, 2012 at 10:45 PM, Justin A. Lemkul jalem...@vt.edu wrote: Hovakim Grabski wrote: Hi, Anyone know any ligand- ligand tutorial? If there is no receptor, then there is no ligand ;) I've been trying to set up a taurine simulation with lysophosphatidylcholines (LPC) with no success. Without a description of what you've tried, what hasn't worked, etc then there's not much anyone can suggest. If you've simply got two small molecules you want to simulate together: 1. Obtain topologies for both species and construct a .top that calls a force field and the small molecule topologies 2. Set up the coordinate file such that the two species are arranged how you'd like them in a single box (done with editconf) 3. Solvate and proceed as you would any other simulated system -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/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 -- 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] discrepancy between ED motions and the MD motion
Thanks Tsjerk Can you plz tell me How do we really conclude that an biologically relevant motion or a simple relaxation ( i have followed this approach, i also carried out a elastic netwok modelling based PCA and comapred the lowest mode obtained from EN-NMA with my PC1- Is this a right approach??) Thanks Regards Vijayan.R On Wed, Dec 21, 2011 at 10:51 AM, Tsjerk Wassenaar tsje...@gmail.comwrote: Hi Vijayan R., Eigenvectors are specific up to a sign. So it's not said the start will end up as the negative extreme. It seems your interpolation just shows what happens in reverse. As a sidenote, do check whether it is a biologically relevant motion, or merely relaxation. Cheers, Tsjerk On Dec 21, 2011 4:24 PM, R.S.K.Vijayan biovija...@gmail.com wrote: Hi all I carried out a distance analysis between two domains with respect to time based on the center of mass. Subsequently i also carried out a PCA based essential dynamics to identify the global/biologically relevant motions. The strange and inconsistent result i find here is when i calculate the distance using the MD (progressive fitted) trajectory, I find that the two domains of interest move apart with respect to time. on the contrary a ED followed by a smoothed interpolation between the two extreme motions revelas that the two domains move closer to each other in a concerted fashion. does any one has an explanation for this discrepancy between ED motions and the MD motion ??? Thanking you in advance Regards Vijayan.R On Tue, Dec 20, 2011 at 2:28 AM, bipin singh bipinel...@gmail.com wrote: Thanks a lot for your suggestions. On Mon, Dec 19, 2011 at 21:00, David Mobley dmob...@gmail.com wrote: Yes, changing the net charge of the system is something that is rather complicated in fact (one can plunge ahead and do it while ignoring the complications, but the results will typically be rather system-size dependent and essentially wrong). For more details refer to the Kastenholz and Hunenberger papers from J. Chem. Phys (2006 or 2007) and references therein. The good news is that for simple spherical ions KH have worked out the relevant corrections. The bad news is that if you move away from simple spherical ions you've got problems. David Mobley On Fri, Dec 16, 2011 at 6:41 AM, Justin A. Lemkul jalem...@vt.eduwrote: bipin singh wrote: Hello, I am willing to study the free energy of binding of a cation (Ca++) to the protein and I am following the free energy tutorial provided by Justin (http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin/** gmx-tutorials/free_energyhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy ). Please let me know whether the settings for this type of study would be same as given in the tutorial for ligand-Protein binding free energy calculation or it need some different approach: By decoupling a Ca2+ ion, you are removing 2 charges from the system. I don't know how to properly treat such a case (perhaps someone else can comment), but likely you'll find such topics in the literature. A better approach may be umbrella sampling, but again the literature should point you to reasonable methodology. I'm sure others have dealt with such questions before. -Justin The setting from the ligand-Protein binding free energy calculation are given as: van der Waals coupling: sc-alpha = 0.5 ; use soft-core for LJ (de)coupling sc-sigma = 0.3 sc-power = 1 couple-moltype= LIG couple-intramol = no couple-lambda0= none; non-interacting dummy in state A couple-lambda1= vdw ; only vdW terms on in state B Coulombic coupling: sc-alpha = 0 ; soft-core during (dis)charging can be unstable! sc-sigma = 0 couple-moltype= LIG couple-intramol = no couple-lambda0= vdw ; only vdW terms in state A (the previous state B is now A) couple-lambda1= vdw-q ; all nonbonded interactions are on in state B -- ==**== 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/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
[gmx-users] Eigenvalue values from PCA (a general question)
Hi all I have a query about the eigenvalue values obtained from g_covar and g_anaeig I performed essential dynamics using PCA on my system (Protein-DNA complex) considering BB of the protein and the phosphate and sugar of the DNA for a 50 ns trajectory. The eigenvalue which i do obtain for the top 10 principal components are stated below 1 10.1064 2 4.78616 3 4.07406 4 3.48535 5 2.7176 6 2.13348 7 1.75909 8 1.45699 9 1.12932 10 0.893933 What i infer from this is that the cumulative variance experienced by the top 10 PC is hardly ~ 30 %. so my questions are a) does this imply inadequate sampling by MD or a limited conformational change happening in the system b) is it wise to consider the Nucleic acid during essential dynamics or should it be discared and only the Protein BB or CA be considered. Thanking you in advance for your suggestions. My apologies since it sound to be a very general question and rather not very specific to Gromacs. Regards Vijayan.R -- 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] Eigenvalue values from PCA (a general question)
Hi Tsjerk Many thanks for your response. Do you think NMA is worth considering in such cases like this? Regards Vijayan.R On Thu, Dec 15, 2011 at 3:39 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Vijayan R., What i infer from this is that the cumulative variance experienced by the top 10 PC is hardly ~ 30 %. Not experienced...; It's the variance captured by the first ten PC's. a) does this imply inadequate sampling by MD or a limited conformational change happening in the system No, not at all. It shows that the motions in your system can not be adequately captured by linear combinations of atom fluctuations. The system may be too flexible and/or there may be a lot of rotational motion. b) is it wise to consider the Nucleic acid during essential dynamics or should it be discared and only the Protein BB or CA be considered. Analysis with and without nucleic acids are just two different things. Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- 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] Eigenvalue values from PCA (a general question)
Thanks Tsjerk On Thu, Dec 15, 2011 at 4:55 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Vijayan.R, Not really. NMA also assumes linear relationships. Cheers, Tsjerk On Thu, Dec 15, 2011 at 10:48 PM, R.S.K.Vijayan biovija...@gmail.com wrote: Hi Tsjerk Many thanks for your response. Do you think NMA is worth considering in such cases like this? Regards Vijayan.R On Thu, Dec 15, 2011 at 3:39 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Vijayan R., What i infer from this is that the cumulative variance experienced by the top 10 PC is hardly ~ 30 %. Not experienced...; It's the variance captured by the first ten PC's. a) does this imply inadequate sampling by MD or a limited conformational change happening in the system No, not at all. It shows that the motions in your system can not be adequately captured by linear combinations of atom fluctuations. The system may be too flexible and/or there may be a lot of rotational motion. b) is it wise to consider the Nucleic acid during essential dynamics or should it be discared and only the Protein BB or CA be considered. Analysis with and without nucleic acids are just two different things. Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- 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, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- 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] Re: Eigenvalue values from PCA (a general question)
Thanks Micheal for pointing out the mistake On Fri, Dec 16, 2011 at 4:20 AM, Niesen, Michiel mnie...@coh.org wrote: Date: Thu, 15 Dec 2011 15:11:12 -0500 From: R.S.K.Vijayan biovija...@gmail.com Subject: [gmx-users] Eigenvalue values from PCA (a general question) To: gmx-users@gromacs.org Message-ID: camm9pawrymqrgzheriarvovk7qwuzpfwrm_owc_0+cemezm...@mail.gmail.com Content-Type: text/plain; charset=iso-8859-1 Hi all I have a query about the eigenvalue values obtained from g_covar and g_anaeig I performed essential dynamics using PCA on my system (Protein-DNA complex) considering BB of the protein and the phosphate and sugar of the DNA for a 50 ns trajectory. The eigenvalue which i do obtain for the top 10 principal components are stated below 1 10.1064 2 4.78616 3 4.07406 4 3.48535 5 2.7176 6 2.13348 7 1.75909 8 1.45699 9 1.12932 10 0.893933 What i infer from this is that the cumulative variance experienced by the top 10 PC is hardly ~ 30 %. The cumulative variance described by a set of PCs is not the sum of their eigenvalues. You have to take the sum of the first x eigenvalues as a percentage of the sum of all eigenvalues to get the cumulative variance. a) does this imply inadequate sampling by MD or a limited conformational change happening in the system b) is it wise to consider the Nucleic acid during essential dynamics or should it be discared and only the Protein BB or CA be considered. Thanking you in advance for your suggestions. My apologies since it sound to be a very general question and rather not very specific to Gromacs. Regards Vijayan.R - *SECURITY/CONFIDENTIALITY WARNING: This message and any attachments are intended solely for the individual or entity to which they are addressed. This communication may contain information that is privileged, confidential, or exempt from disclosure under applicable law (e.g., personal health information, research data, financial information). Because this e-mail has been sent without encryption, individuals other than the intended recipient may be able to view the information, forward it to others or tamper with the information without the knowledge or consent of the sender. If you are not the intended recipient, or the employee or person responsible for delivering the message to the intended recipient, any dissemination, distribution or copying of the communication is strictly prohibited. If you received the communication in error, please notify the sender immediately by replying to this message and deleting the message and any accompanying files from your system. If, due to the security risks, you do not wish to receive further communications via e-mail, please reply to this message and inform the sender that you do not wish to receive further e-mail from the sender. - -- 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
[gmx-users] Cosine content
Dear Gromacs users I have a question regarding cosine content. I have a 50 ns trajectory and looking at the RMSD plot, i set aside the first 5 ns as the time required for stabilization and subsequently carried out a essential dynamics for the backbone atoms post 5ns. But when i perform a cosine content analysis for the eigen vector 1, i get these strange results a) Performing a g_analyze run using -b 5000 to -e 5 ( ie 5- 50 ns ) produces a cosine value of 0.92 but when i perform a cosine analysis using -b 5000 to -e 25000 ( 5-25ns) i get a cosine value of 0.24 also when i perform a cosine analysis using -b 3 to -- 5(30-50 ns) i get a cosine value of 0.05 so how should i interpret this result, does it imply that all the conformational changes are taking place between 30 to 50 ns or is there some thing wrong with the convergence of the system??? Papers tell that the cosine value does decreases with increased time scale due to enhanced sampling, but strange a 25 ns simulation has a low cosine value on the contrary a 50 ns simulation has an increased cosine value. Regards Vijayan.R On Mon, Dec 12, 2011 at 5:31 PM, Justin A. Lemkul jalem...@vt.edu wrote: Alex Jemulin wrote: Dear all Which is the difference between hydropilic and hydrophobic sas? g_sas computes hydrophobic and hydrophilic surface area based on the absolute value of the partial charge of the atom, which can be adjusted with the -qmax flag. How can give an interpretation to g_sas xvg graph? Interpretation of the results is based on the question being asked and the group being analyzed, things that only you know. What can I find out in it and how can use g_sas to analyze a trajectory? Start by reading g_sas -h. -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/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 -- 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] MM/PBSA Gromacs
Dear Gromacs users Is there any script that does a PB or GB calculation to perform a MM/PB(GB)SA free energy calculation in Gromacs. Similar to the MMPBSA.py script available in Amber. I find a similar question raised by a user a couple of years back. Any successful implementation Vijayan.R On Wed, Nov 30, 2011 at 1:26 PM, Justin A. Lemkul jalem...@vt.edu wrote: 김현식 wrote: Dear Experts, Hi, Is there any tools in gromacs to get Hydrophobic cores of protein ? I suppose that depends on what your definition is, but in all likelihood no, not directly. A program like g_sas can give you nonpolar and polar surface areas as well as volumes and surface atoms, which, through crafty use of index groups, may provide you with something useful. -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/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 -- 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] SASA query
Hi Gromacs Users I have a query regarding g_sas which i intend to use for my MM/PBSA calcualtion i am planing to use g_sas for calculating the SASA using a probe radius of 0.14 nm is this okay ? o secondly ∆Gsolv,np = 0.00542*SASA + 0.92 is this master equation right third and important (1) first i calculate for PTN+water and get the SASA for protein (2 ) i calculate for LIgand +water and get the SAS for Ligand (3) I calculate Ptn+ligand+water and choose PTN+LIgand and get the SASA for P+ L right ??? (4) and the final SASA as *(Delta SASA)=SASA(protein)+SASA(ligand)-SASA(protein+ligand)** is this the right procedure. R.S.K.Vijayan -- 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
