[gmx-users] Re: distance restraint
*file alfadrest.itp* [ distance_restraints ] ; i j ? label funct loup1up2 weight 8002 10641 1 0 10.40.50.6 1 8040 10616 1 0 10.40.50.6 1 8067 10582 1 0 10.40.50.6 1 8104 10554 1 0 10.40.50.6 1 8283 10698 1 0 10.40.50.6 1 8259 10723 1 0 10.40.50.6 1 8222 10764 1 0 10.40.50.6 1 8189 10794 1 0 10.40.50.6 1 *file topol.top* ; Include Distance restraint file #ifdef DISRES #include "alfadrest.itp" #endif ; Include Position restraint file #ifdef POSRES #include "posre.itp" #endif ; Include water topology #include "gromos43a1.ff/spc.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include "gromos43a1.ff/ions.itp" [ system ] ; Name Protein [ molecules ] ; Compound#mols Protein_chain_A 1 *file .mdp* ; LINES STARTING WITH ';' ARE COMMENTS title = Minimization ; Title of run define = -DDISRES ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 10.0 ; Stop minimization when the maximum force < 1.0 kJ/mol emstep = 0.01 ; Energy step size nsteps = 50; Maximum number of (minimization) steps to perform energygrps = Protein ; Which energy group(s) to write to disk ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list and long range forces ns_type = grid ; Method to determine neighbor list (simple, grid) rlist = 1.0 ; Cut-off for making neighbor list (short range forces) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb= 1.0 ; long range electrostatic cut-off rvdw= 1.0 ; long range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions (yes/no) ;Parametros distance restraint disre = simple; simple (per-molecule) distance restraints disre_fc= 1000 ; Force constant for distance restraints *Questions* 1.When I am doing the minimization it comes out this message: /Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax < 10 Double precision normally gives you higher accuracy. Steepest Descents converged to machine precision in 349 steps, but did not reach the requested Fmax < 10. / What this implies, can i continue besides this message?Or it is better to do something about it? 2.Can you recomend considerable literature on vacuum simulation? -- View this message in context: http://gromacs.5086.n6.nabble.com/distance-restraint-tp5001387p5001391.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] distance restraint
On 9/27/12 12:04 PM, Paula Andrea Delgado Pinzon wrote: Hello gromacs users, I am doing energy minimization of a big protein with distance restraint (i need to create interactions between a group of residues, so i need them to be close), but in the resultant pdb a don't see those residues close, so how can I verify that the distance restraint are working?. Another unrelated question, is that i am doing the simulation in vacumm, also in this case i need to neutralized the system?, because with the command genion i need solvent to replace by ions, so in this case i can't do that part. There should be a distance restraint energy term printed to the .log file when using distance restraints. If you need help troubleshooting, we will need to see your topology section specifying the [distance_restraints] and your .mdp file. For simple energy minimization, your outcome is probably not going to be heavily impacted by net charge. If you plan on conducting any simulations in vacuo, refer to the considerable literature on this topic for methodology. -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] g_clustsize
On 9/27/12 2:47 PM, mohammad agha wrote: Dear Gromacs users I have one big problem with g_clustsize! I see 9 micelles in my system after running. When I use g_clustsize for number of clusters and average cluster size, they don't emphasize each other, and I see 9 micelles from 36 ps to 120 ps in my box, but results of nclust.xvg is not regular and have very fluctuations. I examine these results in different -cut. Please see my results: nclust.xvg 9.24e+05 11 9.30e+05 11 9.36e+05 9 9.42e+05 7 9.48e+05 5 9.54e+05 6 9.60e+05 16 9.66e+05 13 9.72e+05 13 9.78e+05 12 9.84e+05 9 9.90e+05 12 9.96e+05 7 1.002000e+06 13 1.008000e+06 10 1.014000e+06 5 1.02e+06 8 1.026000e+06 4 1.032000e+06 5 1.038000e+06 10 1.044000e+06 10 1.05e+06 8 1.056000e+06 9 1.062000e+06 8 1.068000e+06 5 1.074000e+06 12 1.08e+06 11 1.086000e+06 8 1.092000e+06 8 1.098000e+06 9 1.104000e+06 10 1.11e+06 8 1.116000e+06 10 1.122000e+06 8 1.128000e+06 4 1.134000e+06 5 1.14e+06 10 1.146000e+06 10 1.152000e+06 11 1.158000e+06 10 1.164000e+06 7 1.17e+06 6 1.176000e+06 4 1.182000e+06 14 1.188000e+06 8 1.194000e+06 2 1.20e+06 6 and avclust.xvg: 9.84e+05 83.333 9.90e+05 62.500 9.96e+05 107.143 1.002000e+06 57.692 1.008000e+06 75.000 1.014000e+06 150.000 1.02e+06 93.750 1.026000e+06 187.500 1.032000e+06 150.000 1.038000e+06 75.000 1.044000e+06 75.000 1.05e+06 93.750 1.056000e+06 83.333 1.062000e+06 93.750 1.068000e+06 150.000 1.074000e+06 62.500 1.08e+06 68.182 1.086000e+06 93.750 1.092000e+06 93.750 1.098000e+06 83.333 1.104000e+06 75.000 1.11e+06 93.750 1.116000e+06 75.000 1.122000e+06 93.750 1.128000e+06 187.500 1.134000e+06 150.000 1.14e+06 75.000 1.146000e+06 75.000 1.152000e+06 68.182 1.158000e+06 75.000 1.164000e+06 107.143 1.17e+06 125.000 1.176000e+06 187.500 1.182000e+06 53.571 1.188000e+06 93.750 1.194000e+06 375.000 1.20e+06 125.000 Whereas the size of clusters in the box are similar when I see with ngmx. I don't know where is my problem!!! I don't see anything that indicates a problem. Your average over the snippet of nclust.xvg is 8.7, which is consistent with your observations. I don't understand what the complaint is about the data in avclust.xvg. -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
[gmx-users] g_clustsize
Dear Gromacs users I have one big problem with g_clustsize! I see 9 micelles in my system after running. When I use g_clustsize for number of clusters and average cluster size, they don't emphasize each other, and I see 9 micelles from 36 ps to 120 ps in my box, but results of nclust.xvg is not regular and have very fluctuations. I examine these results in different -cut. Please see my results: nclust.xvg 9.24e+05 11 9.30e+05 11 9.36e+05 9 9.42e+05 7 9.48e+05 5 9.54e+05 6 9.60e+05 16 9.66e+05 13 9.72e+05 13 9.78e+05 12 9.84e+05 9 9.90e+05 12 9.96e+05 7 1.002000e+06 13 1.008000e+06 10 1.014000e+06 5 1.02e+06 8 1.026000e+06 4 1.032000e+06 5 1.038000e+06 10 1.044000e+06 10 1.05e+06 8 1.056000e+06 9 1.062000e+06 8 1.068000e+06 5 1.074000e+06 12 1.08e+06 11 1.086000e+06 8 1.092000e+06 8 1.098000e+06 9 1.104000e+06 10 1.11e+06 8 1.116000e+06 10 1.122000e+06 8 1.128000e+06 4 1.134000e+06 5 1.14e+06 10 1.146000e+06 10 1.152000e+06 11 1.158000e+06 10 1.164000e+06 7 1.17e+06 6 1.176000e+06 4 1.182000e+06 14 1.188000e+06 8 1.194000e+06 2 1.20e+06 6 and avclust.xvg: 9.84e+05 83.333 9.90e+05 62.500 9.96e+05 107.143 1.002000e+06 57.692 1.008000e+06 75.000 1.014000e+06 150.000 1.02e+06 93.750 1.026000e+06 187.500 1.032000e+06 150.000 1.038000e+06 75.000 1.044000e+06 75.000 1.05e+06 93.750 1.056000e+06 83.333 1.062000e+06 93.750 1.068000e+06 150.000 1.074000e+06 62.500 1.08e+06 68.182 1.086000e+06 93.750 1.092000e+06 93.750 1.098000e+06 83.333 1.104000e+06 75.000 1.11e+06 93.750 1.116000e+06 75.000 1.122000e+06 93.750 1.128000e+06 187.500 1.134000e+06 150.000 1.14e+06 75.000 1.146000e+06 75.000 1.152000e+06 68.182 1.158000e+06 75.000 1.164000e+06 107.143 1.17e+06 125.000 1.176000e+06 187.500 1.182000e+06 53.571 1.188000e+06 93.750 1.194000e+06 375.000 1.20e+06 125.000 Whereas the size of clusters in the box are similar when I see with ngmx. I don't know where is my problem!!! May I ask you to help me Please? Best Regards Sara -- 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] distance restraint
Hello gromacs users, I am doing energy minimization of a big protein with distance restraint (i need to create interactions between a group of residues, so i need them to be close), but in the resultant pdb a don't see those residues close, so how can I verify that the distance restraint are working?. Another unrelated question, is that i am doing the simulation in vacumm, also in this case i need to neutralized the system?, because with the command genion i need solvent to replace by ions, so in this case i can't do that part. Thanks for your help Paula -- 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] tau_t and tc_grps for v-rescale
Hi, I'd greatly appreciate any general advice on the possibility to use several (2 or more) tc_grps with v-rescale and how large could be tau_t with this coupling method (is 0.3 ps still OK?). Many thanks in advance and best regards, Felipe -- 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] g_tcaf segmentation fault
The .trr file can contain coordinates, velocities, and forces over time, depending on your .mdp settings (nstxout, nstvout, nstfout). For g_tcaf, you need to have velocities. It does say so in the manpage. Run gmxcheck to see what's in your .trr file. A segmentation fault with the analysis tools is usually an indication that there is a mismatch in data, e.g. between trajectory and reference structure, or that some data is missing, like velocities in a trajectory. Of course the developers could try and catch all those things, but they rather spend their time thinking of new things :p Cheers, Tsjerk On Thu, Sep 27, 2012 at 2:18 PM, Stelios Karozis wrote: > Sorry, but i was wrong, the .trr file contains trajectories and the .gro > output file contains velocities as it should. > > Stelios > > > On 09/27/2012 03:03 PM, Stelios Karozis wrote: >> >> Hi Tsjerk, >> I checked my .trr file and it contains the velocities, as it should. >> >> Stelios >> On 09/27/2012 09:12 AM, Tsjerk Wassenaar wrote: >>> >>> Hi Stelios, >>> >>> Does your .trr file contain velocities? >>> >>> Cheers, >>> >>> Tsjerk >>> >>> On Sep 26, 2012 8:24 PM, "Stelios Karozis" >>> wrote: >>> >>> Thanks for the response. First i tried the .trr from the simulation and >>> the >>> result was segmentation fault. >>> I use g_covar for entropy estimation combined with g_anaeig command. So >>> the >>> use of g_covar .trr file as an input, was easy alternative .trr file to >>> see >>> if i will get pass the segmantation fault error. I didn t give it too >>> much >>> thought. >>> >>> Stelios >>> >>> Ο χρήστης Justin Lemkul έγραψε: >>> >>> On 9/26/12 12:55 PM, Stelios Karozis wrote: > Thanks for the suggestion. >>> > >>> I just tried and the p... >>> >>> The trajectory written from g_covar contains eigenvectors from PCA. I >>> don't >>> understand why you wou... >>> >>> -- Justin A. Lemkul, Ph.D. >>> Research Scientist Department ... >> >> > > -- > -- > Stelios Karozis > Research Assistant > Environmental Research Lab > IN-RAS-TES - NCSR Demokritos - Greece > email: skaro...@ipta.demokritos.gr > tel : 0030 210 650 3403 > > -- > 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 Biocomputing Group Department of Biological Sciences 2500 University Drive NW Calgary, AB T2N 1N4 Canada -- 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] g_tcaf segmentation fault
Hi Stelios, But the eigenvec.trr does not. You shouldn't be using that. So what exactly are you doing? How many frames do you have in your .trr file, what do you give for selections, etc? Please paste the exact commands and resulting output. Cheers, Tsjerk On Thu, Sep 27, 2012 at 2:03 PM, Stelios Karozis wrote: > Hi Tsjerk, > I checked my .trr file and it contains the velocities, as it should. > > Stelios > > On 09/27/2012 09:12 AM, Tsjerk Wassenaar wrote: >> >> Hi Stelios, >> >> Does your .trr file contain velocities? >> >> Cheers, >> >> Tsjerk >> >> On Sep 26, 2012 8:24 PM, "Stelios Karozis" >> wrote: >> >> Thanks for the response. First i tried the .trr from the simulation and >> the >> result was segmentation fault. >> I use g_covar for entropy estimation combined with g_anaeig command. So >> the >> use of g_covar .trr file as an input, was easy alternative .trr file to >> see >> if i will get pass the segmantation fault error. I didn t give it too much >> thought. >> >> Stelios >> >> Ο χρήστης Justin Lemkul έγραψε: >> >> On 9/26/12 12:55 PM, Stelios Karozis wrote: > Thanks for the suggestion. > >> I just tried and the p... >> >> The trajectory written from g_covar contains eigenvectors from PCA. I >> don't >> understand why you wou... >> >> -- Justin A. Lemkul, Ph.D. >> Research Scientist Department ... > > > -- > -- > Stelios Karozis > Research Assistant > Environmental Research Lab > IN-RAS-TES - NCSR Demokritos - Greece > email: skaro...@ipta.demokritos.gr > tel : 0030 210 650 3403 > > -- > 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 Biocomputing Group Department of Biological Sciences 2500 University Drive NW Calgary, AB T2N 1N4 Canada -- 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] g_tcaf segmentation fault
Sorry, but i was wrong, the .trr file contains trajectories and the .gro output file contains velocities as it should. Stelios On 09/27/2012 03:03 PM, Stelios Karozis wrote: Hi Tsjerk, I checked my .trr file and it contains the velocities, as it should. Stelios On 09/27/2012 09:12 AM, Tsjerk Wassenaar wrote: Hi Stelios, Does your .trr file contain velocities? Cheers, Tsjerk On Sep 26, 2012 8:24 PM, "Stelios Karozis" wrote: Thanks for the response. First i tried the .trr from the simulation and the result was segmentation fault. I use g_covar for entropy estimation combined with g_anaeig command. So the use of g_covar .trr file as an input, was easy alternative .trr file to see if i will get pass the segmantation fault error. I didn t give it too much thought. Stelios Ο χρήστης Justin Lemkul έγραψε: On 9/26/12 12:55 PM, Stelios Karozis wrote: > Thanks for the suggestion. > I just tried and the p... The trajectory written from g_covar contains eigenvectors from PCA. I don't understand why you wou... -- Justin A. Lemkul, Ph.D. Research Scientist Department ... -- -- Stelios Karozis Research Assistant Environmental Research Lab IN-RAS-TES - NCSR Demokritos - Greece email: skaro...@ipta.demokritos.gr tel : 0030 210 650 3403 -- 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] g_tcaf segmentation fault
Hi Tsjerk, I checked my .trr file and it contains the velocities, as it should. Stelios On 09/27/2012 09:12 AM, Tsjerk Wassenaar wrote: Hi Stelios, Does your .trr file contain velocities? Cheers, Tsjerk On Sep 26, 2012 8:24 PM, "Stelios Karozis" wrote: Thanks for the response. First i tried the .trr from the simulation and the result was segmentation fault. I use g_covar for entropy estimation combined with g_anaeig command. So the use of g_covar .trr file as an input, was easy alternative .trr file to see if i will get pass the segmantation fault error. I didn t give it too much thought. Stelios Ο χρήστης Justin Lemkul έγραψε: On 9/26/12 12:55 PM, Stelios Karozis wrote: > Thanks for the suggestion. > I just tried and the p... The trajectory written from g_covar contains eigenvectors from PCA. I don't understand why you wou... -- Justin A. Lemkul, Ph.D. Research Scientist Department ... -- -- Stelios Karozis Research Assistant Environmental Research Lab IN-RAS-TES - NCSR Demokritos - Greece email: skaro...@ipta.demokritos.gr tel : 0030 210 650 3403 -- 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] Do not want to add hydrogens to intial pdb structure
Specify a united atom forcefield? You can also do a direct conversion from pdb to gro using editconf, but that's not going to generate a topology. On 2012-09-27 03:38:15PM +0530, mohan maruthi sena wrote: > Hi all, > When we generate .gro , .top files using pdb2gmx command it > add hydrogens to the structure depending upon the valency of the atom. Is > there any option in gromacs such that it does not add hydrogens to the > intial structure . > > > Thank you, > Mohan > -- > 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
Re: [gmx-users] rapid change in the angle of simulation cell - regd
Hi Ramesh, Did you note how your atoms didn't change their positions? And how you can still stack them using either set of vectors? It's a great example of how PBC works. It's not the box that's important, not the vectors, but the infinite simulation system that results from stacking the unit cell contents, using the lattice vectors. And there's an infinite number of lattice vectors that give the same result. Not all of these vectors are practical to work with from a computational point of view. What Gromacs does is choosing the vectors that are most convenient to work with, which is laid down in the rules for box vectors given in chapter 3 of the manual. This is called the reduced basis of the lattice. For what you want to do, you need to identify the smallest difference angle between the lattice vectors in your system and your reference. The best way to do that is to work with the reduced basis from the start. Any other set of lattice vectors will give lower difference angles. If you don't really get what I'm writing here, you may want to check Appendix A in http://dissertations.ub.rug.nl/FILES/faculties/science/2006/t.a.wassenaar/03_c3.pdf Hope it helps, Tsjerk On Wed, Sep 26, 2012 at 7:32 AM, ramesh cheerla wrote: > Dear Gromacs users, > > I am performing simulations of a > polymer crystal in Gromacs, for these simulations I have generated a > triclinic box, and have done one step minimization. In the single step > minimization itself the simulation box angle "beta" is varying from > 125.4 degrees to 102 degrees. Decrement of beta value by 23.4 > degrees in single step might not be acceptable. what is the way to > seize this large change in beta value ? > Here I am sending link to the picture of my system with simulation > cell before and after minimization of one step(1fs). > > http://researchweb.iiit.ac.in/~bipin.singh/new.png > > Can anybody please go through the image and provide the reasonable > solution, as the angle variations of the simulation cell are one of > important analyses in my studies. > > > > Thank you in advance, > > Regards, > Ramesh. > -- > 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 Biocomputing Group Department of Biological Sciences 2500 University Drive NW Calgary, AB T2N 1N4 Canada -- 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 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 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 > >> 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 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 >> >> An: Discussion list for GROMACS users >> >> 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 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 >> >> > >> >> > -- >> >> > ==**== >>
