Re: [gmx-users] Density of pure tetrolic acid does not agree with experimental data
Nathan, The experimental data ideally corresponds to an infinitely long, well-converged MD simulation at the corresponding set of temperature and pressure, not after EM and most certainly not after just filling a box, where spacing is according to a preset cut-off and not due to interatomic interactions. Alex NKH Hello Gromacs users, NKH I tried to create a 6.5 nm cubic box of tetrolic acid (otherwise NKH known as 2-butynoic acid), but the density is too low. According NKH to this, http://www.chemspider.com/Chemical-Structure.61810.html, NKH the density should be about 0.964 NKH g/mL. Given the molecular weight of tetrolic acid, this NKH corresponds to right around 1900 molecules in the 6.5 nm box I NKH prepared. Unfortunately, when I attempted to fill the box, NKH Gromacs only found room for 1676 molecules, resulting in NKH a density of 0.852 g/mL. I know that models are not 100% NKH accurate, but I'm worried about a difference that big. Should I NKH expect the system to condense when I minimize, and just shrink NKH the box afterwards? Or do you think there is NKH another problem? NKH Thanks for your help, NKH Nathan -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Density of pure tetrolic acid does not agree with experimental data
Hello Gromacs users, I tried to create a 6.5 nm cubic box of tetrolic acid (otherwise known as 2-butynoic acid), but the density is too low. According to this, http://www.chemspider.com/Chemical-Structure.61810.html, the density should be about 0.964 g/mL. Given the molecular weight of tetrolic acid, this corresponds to right around 1900 molecules in the 6.5 nm box I prepared. Unfortunately, when I attempted to fill the box, Gromacs only found room for 1676 molecules, resulting in a density of 0.852 g/mL. I know that models are not 100% accurate, but I'm worried about a difference that big. Should I expect the system to condense when I minimize, and just shrink the box afterwards? Or do you think there is another problem? Thanks for your help, Nathan -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] fixed number of clusters from a MD simulation
Hi Rebeca, You'd need to use k-means/k-medians clustering for that, which is not in gmx cluster. I'd suggest to perform PCA and collect the projections onto the first ten or so eigenvectors to decrease the dimensionality. This data matrix you can then process with, e.g., R to perform k-means clustering. Cheers, Tsjerk On Mar 31, 2015 2:00 AM, Rebeca García Fandiño rega...@hotmail.com wrote: Dear Gromacs users, I am trying to find a method to obtain a fixed number of clusters (using g_cluster) from a MD simulation. The search of clusters is very manual, depending a lot of the cutoff selected for the analysis. Is there any way to calculate a fixed number of clusters from a MD simulation, in such way that the program calculates the proper cutoff to provide the exact number asked by the user? Best wishes, Rebeca. Dr. Rebeca Garcia Santiago de Compostela University Spain -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Density of pure tetrolic acid does not agree with experimental data
Hi Nathan, Yes, placement of molecules neglects the interactions. You need to simulate the stuff before drawing conclusions. Cheers, Tsjerk On Mar 31, 2015 8:43 AM, Nathan K Houtz nho...@purdue.edu wrote: Hello Gromacs users, I tried to create a 6.5 nm cubic box of tetrolic acid (otherwise known as 2-butynoic acid), but the density is too low. According to this, http://www.chemspider.com/Chemical-Structure.61810.html, the density should be about 0.964 g/mL. Given the molecular weight of tetrolic acid, this corresponds to right around 1900 molecules in the 6.5 nm box I prepared. Unfortunately, when I attempted to fill the box, Gromacs only found room for 1676 molecules, resulting in a density of 0.852 g/mL. I know that models are not 100% accurate, but I'm worried about a difference that big. Should I expect the system to condense when I minimize, and just shrink the box afterwards? Or do you think there is another problem? Thanks for your help, Nathan -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Unexpected trjconv -nojump behaviour
Hi Trayder, The first frames did not have the same position/orientation and/or the same box. Cheers, Tsjerk On Mar 31, 2015 10:00 AM, Trayder Thomas trayder.tho...@monash.edu wrote: Hi, I'm struggling with pbc nojump for a particular starting structure and don't understand why. The system starts with a broken conformation so I've concatenated it onto a whole structure such that the whole structure is the first frame: trjcat -f whole.xtc md1-1.xtc -cat -o test.xtc I then look at the resulting file and it's exactly how I'd expect. I then run trjconv with nojump trjconv -f test.xtc -pbc nojump -o test2.xtc Looking at the output from this, the first frame is fine but on the second frame some residues of my protein that were near the boundary immediately jump to the opposite side of the periodic cell and stay there. When I try to fix that with pbc mol: trjconv -f test2.xtc -pbc mol -s system.tpr -o test3.xtc I find that half of my protein (2 fragments under one molecule type) instead jumps across the system to follow the few stray residues. Any ideas? Thanks, -Trayder -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Unexpected trjconv -nojump behaviour
Hi, I'm struggling with pbc nojump for a particular starting structure and don't understand why. The system starts with a broken conformation so I've concatenated it onto a whole structure such that the whole structure is the first frame: trjcat -f whole.xtc md1-1.xtc -cat -o test.xtc I then look at the resulting file and it's exactly how I'd expect. I then run trjconv with nojump trjconv -f test.xtc -pbc nojump -o test2.xtc Looking at the output from this, the first frame is fine but on the second frame some residues of my protein that were near the boundary immediately jump to the opposite side of the periodic cell and stay there. When I try to fix that with pbc mol: trjconv -f test2.xtc -pbc mol -s system.tpr -o test3.xtc I find that half of my protein (2 fragments under one molecule type) instead jumps across the system to follow the few stray residues. Any ideas? Thanks, -Trayder -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Setting custom atoms in FF
On 3/30/15 10:10 PM, Alex wrote: I am not sure if your answer was a resounding yes. I don't have the time or desire to build something, test it, and give you an absolute answer :) I can only tell you what the code says, which I can do quickly. I am talking about the label on the left in PDB. ...which in this case would have to match the entry in the .n2t Let us say I want to name my atoms TEST1 and TEST2 and set up my PDB as ATOM 1 TEST1 CNT A 1 xxx yyy zzz 1.00 0.00 ATOM 2 TEST2 CNT A 1 xxx yyy zzz 1.00 0.00 and then in atomname2type.a2t I put TEST1 opls_9960 12.011 3C 0.142 C 0.142 C 0.142 TEST2 opls_1001 0.112.011 3C 0.142 C 0.142 C 0.149 will the resulting topology contain the distinction despite the issue with bond lengths? If not, what would be the correct syntax to do that? This should work (sorry, again I can't be resounding in my answer). I just want to define my atoms in a way that supplements (actually, precedes) what x2top does when the atoms are not specifically labeled. A tedious solution in my case, but definitely viable, if this works. Make a toy system. Three C atoms in a line, the bond length between one of them at 0.149 and the other at 0.142, terminal carbons with different names, and an .n2t entry with two lines, specifying these connections. That will tell you if you're on to something or not. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Advice needed
Thankyou Justin. On Tue, Mar 31, 2015 at 5:12 PM, Justin Lemkul jalem...@vt.edu wrote: On 3/31/15 5:25 AM, Priya Das wrote: Dear all, I am working with a transmembrane ion channel and have docked a ligand which binds to its pore. The ligand forms only one hydrogen bond with the ion channel. I want to prove the stability of the binding of this ligand using protein-ligand dynamics. 1) Do i need to convey to the system about the hydrogen bonds , i.e., between which atoms are the hydrogen bonds formed ? Hydrogen bonds arise principally due to electrostatic interactions. You don't provide any sort of information about this is a hydrogen bond as part of any input. 2) Is gmx hbonds the command for it? As the name implies, yes. 3) In the tutorial ( http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ gmx-tutorials/complex/01_pdb2gmx.html) , there is no mention about forming any hydrogen bonds between ligand and protein , then how do we judge that the protein- ligand affinity is stable in that site or in that conformation? Hydrogen bonding is one of many possible stabilizing interactions. There is a whole lot more to the story of protein-ligand binding than just hydrogen bonds. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- *Let us all join hands to save our Mother Earth* Regards, Priya Das Research Scholar Dept. of Computational Biology and Bioinformatics, University of Kerala -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Advice needed
On 3/31/15 5:25 AM, Priya Das wrote: Dear all, I am working with a transmembrane ion channel and have docked a ligand which binds to its pore. The ligand forms only one hydrogen bond with the ion channel. I want to prove the stability of the binding of this ligand using protein-ligand dynamics. 1) Do i need to convey to the system about the hydrogen bonds , i.e., between which atoms are the hydrogen bonds formed ? Hydrogen bonds arise principally due to electrostatic interactions. You don't provide any sort of information about this is a hydrogen bond as part of any input. 2) Is gmx hbonds the command for it? As the name implies, yes. 3) In the tutorial ( http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/01_pdb2gmx.html) , there is no mention about forming any hydrogen bonds between ligand and protein , then how do we judge that the protein- ligand affinity is stable in that site or in that conformation? Hydrogen bonding is one of many possible stabilizing interactions. There is a whole lot more to the story of protein-ligand binding than just hydrogen bonds. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Query- Ligand parametrization
Thank you Justin. On Sun, Mar 29, 2015 at 8:50 AM, Justin Lemkul jalem...@vt.edu wrote: On 3/28/15 8:36 AM, Priya Das wrote: This is the Paramchem generated file. * Toppar stream file generated by * CHARMM General Force Field (CGenFF) program version 0.9.7.1 beta * For use with CGenFF version 2b8 * read rtf card append * Topologies generated by * CHARMM General Force Field (CGenFF) program version 0.9.7.1 beta * using valence-based bond orders * 36 1 ! penalty is the highest penalty score of the associated parameters. ! Penalties lower than 10 indicate the analogy is fair; penalties between 10 ! and 50 mean some basic validation is recommended; penalties higher than ! 50 indicate poor analogy and mandate extensive validation/optimization. RESI Pose 0.000 ! param penalty= 117.000 ; charge penalty= 37.947 GROUP! CHARGE CH_PENALTY ATOM N NG311 -0.299 ! 37.947 Check interactions with water here; the penalty is not that bad but you'll want to check. ATOM C1 CG311 -0.102 !9.362 ATOM C2 CG311 -0.102 ! 24.826 ATOM C3 CG311 -0.092 ! 12.017 ATOM C4 CG321 -0.181 ! 19.898 ATOM C5 CG321 -0.167 ! 18.342 ATOM C6 CG321 -0.165 !0.000 ATOM C7 CG311 -0.094 ! 17.735 ATOM C8 CG321 -0.183 ! 18.342 ATOM C9 CG321 -0.217 ! 15.714 ATOM H HGPAM1 0.345 !7.962 ATOM C10CG321 -0.184 ! 18.342 ATOM C11CG321 -0.181 ! 15.714 ATOM C12CG331 -0.271 !0.030 ATOM C13CG321 -0.180 !0.030 ATOM C14CG321 -0.176 !0.030 ATOM C15CG331 -0.271 !0.030 ATOM H2 HGA10.090 !1.100 ATOM H3 HGA10.090 !2.536 ATOM H4 HGA10.090 !0.000 ATOM H5 HGA20.090 !0.000 ATOM H6 HGA20.090 !0.000 ATOM H7 HGA20.090 !0.750 ATOM H8 HGA20.090 !0.750 ATOM H9 HGA20.090 !0.000 ATOM H10HGA20.090 !0.000 ATOM H11HGA10.090 !2.536 ATOM H12HGA20.090 !0.750 ATOM H13HGA20.090 !0.750 ATOM H14HGA20.090 !0.000 ATOM H15HGA20.090 !0.000 ATOM H16HGA20.090 !0.750 ATOM H17HGA20.090 !0.750 ATOM H18HGA20.090 !0.000 ATOM H19HGA20.090 !0.000 ATOM H20HGA30.090 !0.000 ATOM H21HGA30.090 !0.000 ATOM H22HGA30.090 !0.000 ATOM H23HGA20.090 !0.000 ATOM H24HGA20.090 !0.000 ATOM H25HGA20.090 !0.000 ATOM H26HGA20.090 !0.000 ATOM H27HGA30.090 !0.000 ATOM H28HGA30.090 !0.000 ATOM H29HGA30.090 !0.000 ! Bond order BOND NH! 1 BOND NC2 ! 1 BOND NC7 ! 1 BOND C1 C4 ! 1 BOND C1 C3 ! 1 BOND C1 C2 ! 1 BOND C2 C5 ! 1 BOND C3 C13 ! 1 BOND C3 C6 ! 1 BOND C4 C8 ! 1 BOND C5 C9 ! 1 BOND C6 C9 ! 1 BOND C7 C8 ! 1 BOND C7 C10 ! 1 BOND C10 C11 ! 1 BOND C11 C12 ! 1 BOND C13 C14 ! 1 BOND C14 C15 ! 1 BOND C1 H2 ! 1 BOND C2 H3 ! 1 BOND C3 H4 ! 1 BOND C4 H5 ! 1 BOND C4 H6 ! 1 BOND C5 H7 ! 1 BOND C5 H8 ! 1 BOND C6 H9 ! 1 BOND C6 H10 ! 1 BOND C7 H11 ! 1 BOND C8 H12 ! 1 BOND C8 H13 ! 1 BOND C9 H14 ! 1 BOND C9 H15 ! 1 BOND C10 H16 ! 1 BOND C10 H17 ! 1 BOND C11 H18 ! 1 BOND C11 H19 ! 1 BOND C12 H20 ! 1 BOND C12 H21 ! 1 BOND C12 H22 ! 1 BOND C13 H23 ! 1 BOND C13 H24 ! 1 BOND C14 H25 ! 1 BOND C14 H26 ! 1 BOND C15 H27 ! 1 BOND C15 H28 ! 1 BOND C15 H29 ! 1 END read param card flex append * Parameters generated by analogy by * CHARMM General Force Field (CGenFF) program version 0.9.7.1 beta * ! Penalties lower than 10 indicate the analogy is fair; penalties between 10 ! and 50 mean some basic validation is recommended; penalties higher than ! 50 indicate poor analogy and mandate extensive validation/optimization. BONDS CG311 CG311 222.50 1.5000 ! PROT alkane update, adm jr., 3/2/92 CG311 CG321 222.50 1.5380 ! PROT alkane update, adm jr., 3/2/92 CG311 NG311 263.00 1.4740 ! Pose , from CG321 NG311, PENALTY= 4 CG311 HGA1309.00 1.1110 ! PROT alkane update, adm jr., 3/2/92 CG321 CG321 222.50 1.5300 ! PROT alkane update, adm jr., 3/2/92 CG321 CG331 222.50 1.5280 ! PROT alkane update, adm jr., 3/2/92 CG321 HGA2309.00 1.1110 ! PROT alkane update, adm jr., 3/2/92 CG331 HGA3322.00 1.1110 ! PROT alkane update, adm jr., 3/2/92 NG311 HGPAM1 447.80 1.0190 ! AMINE aliphatic amines Bonds are OK. ANGLES CG311 CG311 CG31153.35111.008.00 2.56100 ! PROT alkane update, adm jr., 3/2/92 CG311 CG311 CG32153.35111.008.00 2.56100 ! PROT alkane update, adm jr., 3/2/92 CG311 CG311 NG31143.70112.20 ! Pose , from CG331 CG321 NG311, PENALTY= 5.5 CG311 CG311 HGA1
[gmx-users] Advice needed
Dear all, I am working with a transmembrane ion channel and have docked a ligand which binds to its pore. The ligand forms only one hydrogen bond with the ion channel. I want to prove the stability of the binding of this ligand using protein-ligand dynamics. 1) Do i need to convey to the system about the hydrogen bonds , i.e., between which atoms are the hydrogen bonds formed ? 2) Is gmx hbonds the command for it? 3) In the tutorial ( http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/01_pdb2gmx.html) , there is no mention about forming any hydrogen bonds between ligand and protein , then how do we judge that the protein- ligand affinity is stable in that site or in that conformation? -- *Let us all join hands to save our Mother Earth* Regards, Priya Das Research Scholar Dept. of Computational Biology and Bioinformatics, University of Kerala -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Installation problem on CRAY XC40----Gromacs-5.0.4
Nothing unexpected, you can't run on the login node binaries that you compiled for the compute nodes. -- Szilárd On Tue, Mar 31, 2015 at 7:48 AM, Satyabrata Das satyabrata...@gmail.com wrote: Thank you, I will read Cray docs again, presently trying to install with gcc 4.8 because 4.9 is showing incompatibility error with the available cudatoolkit. It seems CPU-only installation is successful. However both built in test case and regression-test failed with the following error: [Tue Mar 31 00:44:27 2015] [c1-0c0s1n1] Fatal error in MPI_Init: Other MPI error, error stack: MPIR_Init_thread(506): MPID_Init(192)...: channel initialization failed MPID_Init(569)...: PMI2 init failed: 1 Kindly help, With best regards, Satyabrata Das -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] g_cluster (gromos method) creates clusters with members having RMSD greater than the cutoff to the cluster middle
I think it _may_ even be more serious than what Christopher reported. The center of the cluster (as defined by Daura et al. and not the middle structure calculated by g_cluster) may not even be outputted with the cluster that was generated from it. This is due to the way the algorithm from Daura et al. is implemented on g_cluster (gromos method). The neighbour list based on the cut-off is constructed only once and is stored in the nnb[] structure. After that structure is sorted (qsort) by the number of neighbours (nnb[].nr), the top-ranked neighbour row (nnb[0].nb) is outputted as a (first) cluster, just like the original article says. After this, as the original article states, the structures of this cluster [must be] eliminated from the pool of structures for the process to be repeated, and I think here is where the implementation diverges from the original algorithm. One way of doing this correctly would be be to construct a new neighbour list based on the structures left, but I guess that, although correct, it would lead to unnecessary calculations. The current implementation on g_cluster does the structure elimination by removing the (first) cluster structures from the nnb[].nb arrays, which store all the neighbours. What may not be evident is that the neighbour rows constructed based on the structures marked for removal should also disappear, because they may be outputted as phantom clusters built from a structures that are already part of other clusters. A quick test to prove that the method is poorly implemented is to save the center of the cluster for later output. With this output, one can see that, for many of the less populated clusters, the center of the cluster is not even part of the cluster. In practice, due to circumstances unknown to me, it seems like it does not affect much the clusters outputted (from a test case I have), which explains why this has passed unnoticed. I only noticed it because I had a very weird cluster with average RMSD higher than the cut-off, which lead me to these diggings. After correcting the code according to my findings, that weird cluster turned out to be two clusters (it was a phantom cluster). So, for someone who may be dealing with similar issues, this may be their source. Going back to the redmine filed by Christopher: for the sake of keeping the analyze_clusters function fairly general, I think the middle structure should be the one being outputted to the .log (and etc). But maybe the function can be updated to use the method variable and, in the case of gromos, output the center of the clusters to stderr as a warning? Just an idea. Cheers, João PS: This was based on version 4.6.7. A quick diff against 5.0.4 shows nothing changed in the gromos function of the gmx_cluster.c, so it applies to version 5 too. PSS: The gromos function has an unnecessary variable row being declared, with memory being allocated and freed, without anything happening in the middle. It can be removed. On Sat, Feb 14, 2015 at 3:44 AM, Christopher Neale chris.ne...@alum.utoronto.ca wrote: Dear Users: I have sorted out the issue and filed a redmine: http://redmine.gromacs.org/issues/1688 From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Christopher Neale chris.ne...@alum.utoronto.ca Sent: 12 February 2015 22:53 To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] g_cluster (gromos method) creates clusters with members having RMSD greater than the cutoff to the cluster middle Dear Users: I have run g_cluster from gromacs 4.6.5 as follows: g_cluster -s my.tpr -f tmp.xtc -method gromos -nofit -o rmsd-clust_nofit.xpm -g cluster_nofit.log -sz clust-size_nofit.xvg -cl clusters_nofit.pdb -n index.ndx -cutoff 0.275 -wcl 10 -cl finally.xtc The top of cluster_nofit.log looks like this: Using gromos method for clustering Using RMSD cutoff 0.275 nm The RMSD ranges from 0.0247008 to 5.03412 nm Average RMSD is 0.45568 Number of structures for matrix 12391 Energy of the matrix is 4177.11 nm Found 874 clusters Writing middle structure for each cluster to finally.xtc Writing all structures for the first 10 clusters with more than 1 structures to finally.xtc%03d.xtc cl. | #st rmsd | middle rmsd | cluster members 1 | 4219 0.202 | 784700 .154 | 92900 103300 116100 125900 126500 133000 156600 ... | | | 693900 694000 694200 694300 694600 694700 695700 ... So the frame at 694700 is in the first cluster. However, when I use g_rms to look at the rmsd between frame at 784700 and 694700, I find that the RMSD is 0.29 nm. I am confused because frame 784700 is listed as the middle (which I assume is the cluster centroid) so frame 694700 should not be included in this cluster. When I put these two frames into a single .xtc with only 2 frames, g_cluster correctly puts them into two different
Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 131, Issue 130
Re: [gmx-users] Installation problem on CRAY XC40Gromacs-5.0.4 Thank you once again, happy to know that installation is correct. Actually during this installation I have not used cc/CC compiler wrapper scripts. Presently I am trying to compile with MPI GPU=on and tried to specify compiler wrapper scripts by: set CC=cc set CXX=CC and then -DCMAKE_C_COMPILER=cc -DCMAKE_CXX_COMPILER=CC = -- The C compiler identification is GNU 4.8.0 -- The CXX compiler identification is GNU 4.8.0 -- Check for working C compiler: /opt/cray/craype/2.2.1/bin/cc -- Check for working C compiler: /opt/cray/craype/2.2.1/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /opt/cray/craype/2.2.1/bin/CC -- Check for working CXX compiler: /opt/cray/craype/2.2.1/bin/CC -- works Is it correct? The cmake stage completed successfully. However in 'make' stage showing error (attached below) and installation stopped. Don't know what to try. Any hint in this regard will definitely help to progress further. With best regards, Satyabrata Das === Building NVCC (Device) object src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/cuda_tools_generated_pmalloc_cuda.cu.o Building NVCC (Device) object src/gromacs/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir/gpu_utils_generated_gpu_utils.cu.o Building NVCC (Device) object src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/cuda_tools_generated_copyrite_gpu.cu.o Scanning dependencies of target mdrun_objlib Building NVCC (Device) object src/gromacs/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir/gpu_utils_generated_memtestG80_core.cu.o Scanning dependencies of target view_objlib Building NVCC (Device) object src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/cuda_tools_generated_cudautils.cu.o CMake Error at cuda_tools_generated_copyrite_gpu.cu.o.cmake:206 (message): Error generating /home/proj/14/physatya/c40/gromacs-5.0.4/build-intel-mkl-mpi/src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_copyrite_gpu.cu.o make[2]: *** [src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/cuda_tools_generated_copyrite_gpu.cu.o] Error 1 make[2]: *** Waiting for unfinished jobs CMake Error at gpu_utils_generated_gpu_utils.cu.o.cmake:206 (message): Error generating /home/proj/14/physatya/c40/gromacs-5.0.4/build-intel-mkl-mpi/src/gromacs/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//./gpu_utils_generated_gpu_utils.cu.o CMake Error at gpu_utils_generated_memtestG80_core.cu.o.cmake:206 (message): Error generating /home/proj/14/physatya/c40/gromacs-5.0.4/build-intel-mkl-mpi/src/gromacs/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//./gpu_utils_generated_memtestG80_core.cu.o CMake Error at cuda_tools_generated_pmalloc_cuda.cu.o.cmake:206 (message): Error generating /home/proj/14/physatya/c40/gromacs-5.0.4/build-intel-mkl-mpi/src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_pmalloc_cuda.cu.o make[2]: *** [src/gromacs/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir/gpu_utils_generated_gpu_utils.cu.o] Error 1 make[2]: *** Waiting for unfinished jobs On Tue, Mar 31, 2015 at 9:08 PM, gromacs.org_gmx-users-requ...@maillist.sys.kth.se wrote: Send gromacs.org_gmx-users mailing list submissions to gromacs.org_gmx-users@maillist.sys.kth.se To subscribe or unsubscribe via the World Wide Web, visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or, via email, send a message with subject or body 'help' to gromacs.org_gmx-users-requ...@maillist.sys.kth.se You can reach the person managing the list at gromacs.org_gmx-users-ow...@maillist.sys.kth.se When replying, please edit your Subject line so it is more specific than Re: Contents of gromacs.org_gmx-users digest... Today's Topics: 1. Re: Setting custom atoms in FF (Justin Lemkul) 2. Re: Advice needed (Justin Lemkul) 3. Re: Advice needed (Priya Das) 4. Re: Installation problem on CRAY XC40Gromacs-5.0.4 (Szil?rd P?ll) 5. Re: Normal mode analysis (Leandro Bortot) 6. Re: [gmx-developers] Problem with creating a topolgy from PDB file (Justin Lemkul) -- Message: 1 Date: Tue, 31 Mar 2015 07:40:23 -0400 From: Justin Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-us...@gromacs.org Subject: Re: [gmx-users] Setting custom atoms in FF Message-ID: 551a87a7.5060...@vt.edu Content-Type: text/plain; charset=windows-1252; format=flowed On 3/30/15 10:10 PM, Alex wrote: I am not sure if your answer was a resounding yes. I don't have the time or desire to build something, test it, and give you an absolute answer :) I can only tell you what the code says, which I can
Re: [gmx-users] Unexpected trjconv -nojump behaviour
Hi Trayder, The box is identical (copy+pasted), the orientation varies no more than one would expect frame to frame (membrane protein). There is a 20 A jump between the first and second frame but shouldn't -nojump still be keeping the protein whole? The idea of what jumped may change quite a bit if you have a 2nm shift. Also, nojump only keeps things whole if the molecules are whole up to PBC shifts. And they aren't as you find from your output. And shouldn't -pbc mol be keeping my molecule together? Even if its doing it by fragments, I can't reason why it would take a fragment almost completely inside the box (1% atoms outside) and place it on the opposite side of the system. The routine takes the first atom and then sees whether following atoms need to be moved over. I realise the system is trickier than most because its a rhombic dodecahedron with the protein fitting quite tightly, but I've run dozens of batches of simulations and only 2 are causing me any trouble. I can only assume I'm making some invalid assumptions about how the commands work. Probably. The routines are quite clear (and simple, and bugfree). This usually means there is a mismatch somewhere, between reference and trajectory or between successive frames. Try these two things: Visualize the .tpr and the first frames with the box and see what unjumping could do. Extract the original first frame from the trajectory and make that whole, then use that as reference with -pbc nojump. Cheers, Tsjerk -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Fwd: A doubt from topology creation in Gromacs
-- Forwarded message -- From: Rakesh Pant rakesh...@live.com Date: Apr 1, 2015 1:13 AM Subject: A doubt from topology creation in Gromacs To: tsje...@gmail.com tsje...@gmail.com Cc: Dear Tsjerk, I got your email id from gromacs user list. I have a doubt from gromacs topology creation, on dihedral coefficients. Suppose we have, and angle A-B-C-D, and we have parameters for this one dihedral angle: n Vn f1 1 -2.64 0.0 2 -0.811 0.0 3 0.949 0.0 (Vn=Vn/2*(1+cos(n*chi + f1)), ; Vn kcal/mole ; fn: degrees. How can we use these parameter to get dihedral coefficients to use in gromacs with fucntion 3. Or else if we use it with fucntion 1 can we take any one of the three values given. Thanks, Rakesh -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Setting custom atoms in FF
Another question about x2top. The directives I am putting in ffbonded explicitly state that my angle is of type 2 (G96). Why is it reverting to its default value of 1 in the output topology? It wasn't a problem before, when I was just testing a graphene sheet. Now, it's turning into a mess... I know x2top has limited intelligence, but how is this correct program behavior? Also, is there any way to tell x2top to copy all bond and angle parameters from the ff data into the topology the way pdb2gmx does? Thanks, Alex -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] [gmx-developers] Problem with creating a topolgy from PDB file
Please do not post usage questions on the developers' list. I am CC'ing this over to gmx-users; please continue any discussion there. On 3/31/15 11:36 AM, Asmaa El khodary wrote: Hi, I'm a new user of gromacs and I follow some tutorials to run a simulation of lysozyme using OPLS-AA/L force field . The problem is: when I type the command *pdb2gmx -f 1LYD.pdb -water tip3p *in the terminal and choose the force field ,I get this error Program pdb2gmx, VERSION 5.0.4 Source code file: /home/asmaa/Downloads/gromacs-5.0.4/src/gromacs/fileio/futil.cpp, line: 545 File input/output error: 1LYD.pdb An I/O error means the file isn't in your working directory (or, less likely, the file isn't readable to you). List your files to verify. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Environmental variable setting for gmx 5.0.4
Dear gmx, I have installed the gmx in my ubuntu and centos system and tried to set the environmental variable path in-order to use without mentioning the source commend in my terminal of linux. I tried to set my path as follows but couldn't success it. export PATH=/usr/local/gromacs/bin/:$PATH my which gmx shows the following installed path /usr/local/gromacs/bin//gmx I only able to obtain the gmx as every time by mentioning source /usr/local/gromacs/bin/GMXRC Please advice me how do make gmx to work in default in all terminal ? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Setting custom atoms in FF
Building things is not necessary. I just wasn't sure what particular field in PDB you were talking about. Some indication that it is supposed to work is enough. ;) Thanks, Alex JL I don't have the time or desire to build something, test it, and give you an JL absolute answer :) I can only tell you what the code says, which I can do quickly. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Normal mode analysis
Hi Rahul, Did you make the vacuum minimization with a double-precision version of gromacs using the L-BFGS algorithm? From the protocol you described it seems you didn't do it.. What was the maximum force after the minimization? (check the .log file) I hope it helps, Leandro. On Sat, Mar 28, 2015 at 7:26 AM, rahul dhakne rahuldhakn...@gmail.com wrote: Dear all Gromacs user, I am trying to perform the Normal Mode Analysis protein-DNA complex in vacuum. As the complex is highly negative charge (-163)I performed the energy minimization of complex in water (to neutralize the complex). After I get the completely minimized complex, again I have done energy minimization of complex (in vacuum) for just one step to get the .trr input file for the Normal mode analysis. As I have to perform the normal mode analysis in vacuum I did that. But due to highly negative charge it got stuck in hessian matrix calculation. Even though it calculate the matrix I got negative eigenvalues after diagonalizing the matrix. I also tried with complete energy minimization in vacuum and proceed for normal mode calculation, but again stuck with the same problem i.e. high negative charge (-163) How can I neutralize the system?? or there is any way to do that or probably I am doing something unusual?? Any suggestions will be very welcomed. Thanking you in advance! - Rahul -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Hamiltonian replica exchange with umbrella sampling
Hi, I have come to understand that this might be doable with the newest gromacs versions 5.x (and without plumed). Can someone verify this? And if yes would he/she be so kind as to provide a sample .mdp file demonstrating how the pull code and the free energy code are communicating to succeed this? This restraint-lambdas option seems to be the best candidate for the solution and although I understand its purpose in the context of alchemical calculations, I can't figure out a way to use it in an umbrella sampling simulation. Best Maria -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Unexpected trjconv -nojump behaviour
The box is identical (copy+pasted), the orientation varies no more than one would expect frame to frame (membrane protein). There is a 20 A jump between the first and second frame but shouldn't -nojump still be keeping the protein whole? And shouldn't -pbc mol be keeping my molecule together? Even if its doing it by fragments, I can't reason why it would take a fragment almost completely inside the box (1% atoms outside) and place it on the opposite side of the system. In the past I've managed to keep the protein together by running pbc mol whilst centering on a residue at the interface between the two fragments, but that's not working in this case. I realise the system is trickier than most because its a rhombic dodecahedron with the protein fitting quite tightly, but I've run dozens of batches of simulations and only 2 are causing me any trouble. I can only assume I'm making some invalid assumptions about how the commands work. -Trayder On Tue, Mar 31, 2015 at 7:15 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Trayder, The first frames did not have the same position/orientation and/or the same box. Cheers, Tsjerk On Mar 31, 2015 10:00 AM, Trayder Thomas trayder.tho...@monash.edu wrote: Hi, I'm struggling with pbc nojump for a particular starting structure and don't understand why. The system starts with a broken conformation so I've concatenated it onto a whole structure such that the whole structure is the first frame: trjcat -f whole.xtc md1-1.xtc -cat -o test.xtc I then look at the resulting file and it's exactly how I'd expect. I then run trjconv with nojump trjconv -f test.xtc -pbc nojump -o test2.xtc Looking at the output from this, the first frame is fine but on the second frame some residues of my protein that were near the boundary immediately jump to the opposite side of the periodic cell and stay there. When I try to fix that with pbc mol: trjconv -f test2.xtc -pbc mol -s system.tpr -o test3.xtc I find that half of my protein (2 fragments under one molecule type) instead jumps across the system to follow the few stray residues. Any ideas? Thanks, -Trayder -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
