Re: [gmx-users] Inconsistency of multicore simulations in Gromacs 4.5.3
Hi, What do you mean by exactly the same? MD is chaotic, and unless you run mdrun in its reproducible mode, you will not get reproducibility of a trajectory. gmxcheck may help you discover what you have actually got. And you might want to upgrade such a prehistoric version of GROMACS ;-) Mark On Mon, Mar 16, 2015 at 10:49 PM, Fei Zhang f...@vt.edu wrote: Dear all, Sorry to interrupt. I encountered a problem while using Gromacs 4.5.3 with mpi to simulate ionic liquid constrained between two constant charged electrodes. However when I use 1 core and 32 cores to run same simulation (with same .tpr file), the charge density distribution of the first 3000 steps are exactly the same, however later, in about 1 steps, the charge density distribution of 32 cores and 1 core become different. The compiling environment is: 1) gcc/4.7.22) openmpi/1.6.43) fftw/3.3.4(double precision). I am quite confused about it and wonder if anyone else has encountered the same problem. Best Regards, Fei -- 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] Inconsistency of multicore simulations in Gromacs 4.5.3
Dear all, Sorry to interrupt. I encountered a problem while using Gromacs 4.5.3 with mpi to simulate ionic liquid constrained between two constant charged electrodes. However when I use 1 core and 32 cores to run same simulation (with same .tpr file), the charge density distribution of the first 3000 steps are exactly the same, however later, in about 1 steps, the charge density distribution of 32 cores and 1 core become different. The compiling environment is: 1) gcc/4.7.22) openmpi/1.6.43) fftw/3.3.4(double precision). I am quite confused about it and wonder if anyone else has encountered the same problem. Best Regards, Fei -- 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] Forcefield parameters for Zinc
Hi Emma, Just sharing some experience here: I tried to use the AMBER99SB-ILDN forcefield, which has the same Zn parameter as AMBER99SB, for simulating a Zn-binding protein and it was actually not possible to study the Zn-binding process. This happens essentially because it is not a good approximation to consider Zn2+ as a charged sphere and expect it to bind strongly to CysH, or even Cys-, and to His during the simulations because these are not simple charge-charge interactions. Some approaches for better results are to use a tetrahedral model for zinc (Cationic Dummy Atom Approach), use His-Zn and Cys-Zn bonding parameters or to perform QM/MM. I don't know about the tetrahedral model, but using bonding parameters will certainly ensure the bonded state. I believe you can find such parameters for AMBER99SB in the literature. I hope it helps, Leandro. On Mon, Mar 16, 2015 at 9:59 AM, Emma A emma.ahlstr...@lnu.se wrote: Piggot T. T.Piggot@... writes: Hi Mike, As well as the link that Bipin sent, you can also get parameters for GROMOS phosphorylated residues (compatible with the 43A1 force field, I think) from: http://www.gromacs.org/Downloads/User_contributions/Force_fields I've never used either so have no idea which might be better. The ones that Binpin suggested look like they work with the newer GROMOS 54A7 force field, so they might be the ones to use. On your other question, I am not sure about the protein-zinc parameters with a GROMOS force field. I would say, is there any particular need for using one of the GROMOS protein force fields? There are definitely parameters out there for some of the all-atom protein force fields (e.g. AMBER ones) which are probably also better in terms of protein parameters. Cheers Tom PS: Hope things are good in the (relatively) new job! From: gromacs.org_gmx-users-bounces@... [gromacs.org_gmx-users-bounces@...] on behalf of Michael Carter [Michael.Carter@...] Sent: 20 August 2014 12:56 To: gmx-users@... Subject: Re: [gmx-users] Forcefield parameters for Zinc and phosphorylated residues Hi Bipin, Thanks for this. It works well for adding functionality to residues. Cheers, Mike Carter On 20/08/2014 12:10, bipin singh bipinelmat@... wrote: This might help. http://vienna-ptm.univie.ac.at/ *Thanks and Regards,Bipin Singh* On Wed, Aug 20, 2014 at 4:30 PM, Michael Carter Michael.Carter@... wrote: Hi, I have two questions regarding the parameterisation of Zinc ions and a phosphorylated TYR residue within two different protein systems. 1. Zinc parameters: I have three zinc ions within one protein system. I want to use a bonded model so that they do not fly out of my protein upon simulation. Is there any documentation on the parameters for such a model in the GROMOS forcefield? 2. Phosphorylated TYR In another system I have a phosphorylated TYR residue. PDB2GMX does not like this and after looking inot the manual I have found that you can add parameters for this to the existing forcefields. Much like the previous question, is there any documentation on the addition of parameters for phosphorylated residues in the GROMOS forcefield? Any pointers for these questions would be greatly appreciated. Cheers, Mike Carter The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network. -- 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-request@... -- 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-request@... The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message
Re: [gmx-users] Problem in making index.ndx and disres.itp
Hi Justine, As you can see in my .itp file the atom number starts from 1. Even this is the case with index file. I tried to modify index file to have atomic number same as pdb file but it gave a blank output. So my first concern is how GROMACS will know which atom I want to restrain? shall I change the atom number in itp file to corresponding atom number in pdb? My second concern is the second line of my .itp file looks different from the one given in GROMACS website As per GROMACS website: ; ai aj type index type’ low up1 up2 fac in my generated itp: ; i j ? label funct loup1up2 weight So what do you suggest me to do? Thanks in advance. -- Tushar Ranjan Moharana B. Tech, NIT Warangal Ph D Student, CCMB -- 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] error in grompp : No such molecule type Protein
On 3/16/15 6:35 AM, Antara mazumdar wrote: Hi, I am trying to minimise a coarse grained system having DOPC lipid bilayer, a dimeric protein and water. The mdp file has DOPC, Protein and W as coupling groups and my topology file also mentions the number of each correctly. However while running grompp i am getting No such molecule type Protein error. Either the [moleculetype] name is not Protein or you've broken the topology format somehow such that it cannot be correctly parsed. -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] question about g_bundle
dear all i want calculate crossing angle of two helix in membrane, and use g_bundle. but the -na command i do not know what the exact mean. how could i define the -na for calculate the crossing angle of two helix at X-axis? thanks a lot. Cao -- 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] error in grompp : Something is wrong in the coordinate formatting of file system.gro
Hi, I am trying to minimise a coarse grained system having DOPC lipid bilayer, a dimeric protein and water. The mdp file has DOPC, Protein and W as coupling groups and my topology file also mentions the number of each correctly. However while running grompp i am getting *Something is wrong in the coordinate formatting of file system.gro* error. No such molecule type error does not come now. -- *Best,* *Antara* -- J.R.F.(Project) Systems Biology Group CSIR - Institute of Genomics Integrative Biology South Campus, New Delhi-110020 M:+91-9717970040 -- -- 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] KALP-15 in DPPC tutorial
On 3/16/15 12:08 AM, BAOLIN HUANG wrote: Hi All, I am doing the GROMACS Tutorial of KALP-15 in DPPC. Now, I get stuck at Note how many lipids were deleted and update the [ molecules ] directive of your topology accordingly. Run energy minimization. Then, scale down the lipids by a factor of 0.95 (assuming you have used default names, the result of the minimization is called confout.gro): perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5 area_shrink1.dat The command line was gmx grompp -f minim.mdp -c system_inflated.gro -p topol.top -o em.tpr. And I got Fatal error: number of coordinates in coordinate file (system_inflated.gro, 6438) does not match topology (topol.top 888444) I tried to add DPPC 128 in the [ molecules ], however, I You should never, at any point, have 888444 atoms in the system. Likely you've added water to the inflated system. Don't. got Fatal error: No such moleculetype DPPC. How to update the [molecules] in topol.top? And how do I know the number of molecules? You start with 128, InflateGRO prints out how many it removes...then use a text editor. -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] error in grompp : No such molecule type Protein
Hi, I am trying to minimise a coarse grained system having DOPC lipid bilayer, a dimeric protein and water. The mdp file has DOPC, Protein and W as coupling groups and my topology file also mentions the number of each correctly. However while running grompp i am getting No such molecule type Protein error. -- *Best,* *Antara* -- J.R.F.(Project) Systems Biology Group CSIR - Institute of Genomics Integrative Biology South Campus, New Delhi-110020 M:+91-9717970040 -- -- 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_dist
On 3/16/15 6:43 AM, RINU KHATTRI wrote: hello everyone I am working on protein complex with popc membrane gromcs version is 4.5.5 i want to calculate the distance between two residues during the simulation (200ns) i have been made the .ndx file of atoms of two residues and concatenate .xtc file and final .tpr file g_dist -f full.xtc -s final.tpr -n atom.ndx -o dist.xvg Molecule in topology has atom numbers below and above natoms (3893). You are probably trying to use a trajectory which does not match the first 3893 atoms of the run input file. You can make a matching run input file with tpbconv. the indx file is having the atom no which are present in last.gro file kindly help So what does gmxcheck tell you about the contents of the .tpr and the .xtc? Likely you have a mismatch in what you saved to the trajectory either in the run or when using trjconv at some point. -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] error in grompp : Something is wrong in the coordinate formatting of file system.gro
On 3/16/15 7:12 AM, Antara mazumdar wrote: Hi, I am trying to minimise a coarse grained system having DOPC lipid bilayer, a dimeric protein and water. The mdp file has DOPC, Protein and W as coupling groups and my topology file also mentions the number of each correctly. However while running grompp i am getting *Something is wrong in the coordinate formatting of file system.gro* error. No such molecule type error does not come now. So now, instead of having a broken topology (or maybe grompp never even gets that far), you've altered the coordinate file in some way that the format is broken. Without knowing what you're doing or why you're doing it (usually there's no reason to play with the contents of a .gro file manually), there's nothing to say here. -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] Problem in making index.ndx and disres.itp
On 3/16/15 4:36 AM, Tushar Ranjan Moharana wrote: Hi everyone, I wanted to run a distance restricted MD. Since I have many atoms I can't do it manually with a text editor. For that I choose the line corresponding the atom from .pdb file to another text file and rename them as disres.pdb. Then I run the following command to generate disres.itp *gmx genrestr -f disres.pdb -disre -o disres.itp* I got the following out put Which I don't think correct. Please rectify my mistakes Why don't you think it's correct? -Justin My disres.pdb file ATOM936 CG ASP61 -36.433 1.944 57.629 0.7994 1.700 C ATOM937 OD1 ASP61 -37.626 1.784 58.005 -0.8014 1.500 O ATOM938 OD2 ASP61 -35.856 3.065 57.600 -0.8014 1.500 O ATOM 1212 CD2 HIS81 -41.384 3.133 58.251 -0.1141 1.700 C ATOM 1208 CE1 HIS81 -41.090 2.008 60.045 -0.0170 1.700 C ATOM 1211 HE2 HIS81 -39.455 3.044 59.220 0.3911 1.300 H ATOM 1295 CD2 HIS87 -38.577 6.571 57.666 0.1292 1.700 C ATOM 1292 CE1 HIS87 -39.069 5.316 56.005 0.2057 1.700 C ATOM 1294 NE2 HIS87 -39.012 5.303 57.324 -0.5727 1.550 N ATOM 3657 CG ASP 238 -37.842 3.869 61.472 0.7994 1.700 C ATOM 3658 OD1 ASP 238 -37.982 2.630 61.652 -0.8014 1.500 O ATOM 3659 OD2 ASP 238 -37.595 4.399 60.357 -0.8014 1.500 O END My disres.itp file *; distance restraints for SideChain of [ distance_restraints ]; i j ? label funct loup1up2 weight1 2 1 0 1 0.026104 0.226104 1.2261 11 3 1 1 1 0.0261116 0.2261121.22611 11 4 1 2 1 0.412962 0.6129621.61296 11 5 1 3 1 0.424679 0.6246791.62468 11 6 1 4 1 0.2588 0.4588 1.4588 11 7 1 5 1 0.409973 0.6099731.60997 11 8 1 6 10.357780.557781.55778 11 9 1 7 1 0.324584 0.5245841.52458 1110 1 8 1 0.352323 0.5523231.55232 1111 1 9 1 0.336515 0.5365151.53652 1112 110 1 0.284958 0.4849581.48496 12 3 111 1 0.122214 0.3222141.32221 12 4 112 1 0.300036 0.5000361.50004 12 5 113 10.302630.502631.50263 12 6 114 1 0.153161 0.3531611.35316 12 7 115 1 0.389231 0.5892311.58923 12 8 116 1 0.330781 0.5307811.53078 12 9 117 1 0.284293 0.4842931.48429 1210 118 1 0.305142 0.5051421.50514 1211 119 1 0.276073 0.4760731.47607 1212 120 1 0.251726 0.4517261.45173 13 4 121 1 0.456662 0.6566621.65666 13 5 122 1 0.487282 0.6872821.68728 13 6 123 1 0.294685 0.4946851.49469 13 7 124 10.343850.543851.54385 13 8 125 10.323490.523491.52349 13 9 126 1 0.287881 0.4878811.48788 1310 127 1 0.342527 0.5425271.54253 1311 128 10.359650.559651.55965 1312 129 1 0.252203 0.452203 1.4522 14 5 130 1 0.113787 0.3137871.31379 14 6 131 1 0.116054 0.3160541.31605 14 7 132 1 0.347675 0.5476751.54768 14 8 133 1 0.289477 0.4894771.48948 14 9 134 1 0.234584 0.4345841.43458 1410 135 1 0.384379 0.5843791.58438 1411 136 1 0.383668 0.5836681.58367 1412 137 1 0.351603 0.551603 1.5516 15 6 138 1 0.110408 0.3104081.31041 15 7 139 1 0.472676 0.6726761.67268 15 8 140 1 0.459901 0.659901 1.6599 15 9 141 1 0.375173 0.5751731.57517 1510 142 1 0.300614 0.5006141.50061 1511 143 1 0.255373 0.4553731.45537 1512 144 1
Re: [gmx-users] Forcefield parameters for Zinc
Piggot T. T.Piggot@... writes: Hi Mike, As well as the link that Bipin sent, you can also get parameters for GROMOS phosphorylated residues (compatible with the 43A1 force field, I think) from: http://www.gromacs.org/Downloads/User_contributions/Force_fields I've never used either so have no idea which might be better. The ones that Binpin suggested look like they work with the newer GROMOS 54A7 force field, so they might be the ones to use. On your other question, I am not sure about the protein-zinc parameters with a GROMOS force field. I would say, is there any particular need for using one of the GROMOS protein force fields? There are definitely parameters out there for some of the all-atom protein force fields (e.g. AMBER ones) which are probably also better in terms of protein parameters. Cheers Tom PS: Hope things are good in the (relatively) new job! From: gromacs.org_gmx-users-bounces@... [gromacs.org_gmx-users-bounces@...] on behalf of Michael Carter [Michael.Carter@...] Sent: 20 August 2014 12:56 To: gmx-users@... Subject: Re: [gmx-users] Forcefield parameters for Zinc and phosphorylated residues Hi Bipin, Thanks for this. It works well for adding functionality to residues. Cheers, Mike Carter On 20/08/2014 12:10, bipin singh bipinelmat@... wrote: This might help. http://vienna-ptm.univie.ac.at/ *Thanks and Regards,Bipin Singh* On Wed, Aug 20, 2014 at 4:30 PM, Michael Carter Michael.Carter@... wrote: Hi, I have two questions regarding the parameterisation of Zinc ions and a phosphorylated TYR residue within two different protein systems. 1. Zinc parameters: I have three zinc ions within one protein system. I want to use a bonded model so that they do not fly out of my protein upon simulation. Is there any documentation on the parameters for such a model in the GROMOS forcefield? 2. Phosphorylated TYR In another system I have a phosphorylated TYR residue. PDB2GMX does not like this and after looking inot the manual I have found that you can add parameters for this to the existing forcefields. Much like the previous question, is there any documentation on the addition of parameters for phosphorylated residues in the GROMOS forcefield? Any pointers for these questions would be greatly appreciated. Cheers, Mike Carter The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network. -- 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-request@... -- 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-request@... The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network. -- 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-request@... Hi, Related to the Zn-parameters; where can I find the reference (author, journal, year) to the sigma and epsilon (1.95998e-01 5.23000e-02) parameters that I find in /gromacs/top/amber99sb.ff/ffnonbonded.itp for [ atomtypes ] Zn. I would like to use amber99sb force field in my Gromacs simulation of a Zn- containing protein. Best regards, Emma + Join us for an exciting international meeting in Kalmar -
Re: [gmx-users] umbrella sampling tutorial
On 3/15/15 9:57 PM, Ming Tang wrote: Dear Justin, I have tried many cases, and only your code runs smoothly. If I set pull-ngroups = 1, it will warn that pull-group2-name= Chain_A has not been defined. The code you gave me last time runs well. Though the COM between Chain_A and Chain_B remains the same over time, I found that Chain_A does dissociate from the structure and some particles fly away. It's the same, but things move apart? Sorry, this doesn't make sense to me. Do the .mdp settings I provided before recover the behavior of the SMD portion of the tutorial or not? I am trying from the beginning once again and hope to find the reason. Besides, I got another problem. I want to probe the mechanical properties of a triple helix. I tried to fix one side (End) and pull the other side using the umbrella method: ; freeze groups freezegrps = End freezedim = Y Y Y ; COM pulling pull= umbrella pull-geometry = distance pull-dim= Y N N pull-start = yes pull-ngroups= 2 pull-ncoords= 1 pull-coord1-groups = 1 2 pull-group1-name= End pull-group2-name= pull pull-coord1-rate= 0.005 pull-coord1-k = 1000 WARNING: Listed nonbonded interaction between particles 179 and 190 at distance inf which is larger than the table limit 2.437 nm. This is likely either a 1,4 interaction, or a listed interaction inside a smaller molecule you are decoupling during a free energy calculation. Since interactions at distances beyond the table cannot be computed, they are skipped until they are inside the table limit again. You will only see this message once, even if it occurs for several interactions. IMPORTANT: This should not happen in a stable simulation, so there is probably something wrong with your system. Only change the table-extension distance in the mdp file if you are really sure that is the reason. I'd venture a guess here that your system is probably blowing up because you're tugging on one molecule, which reaches a limit, distorts, and the simulation fails. If I just fix one of the three dimensions, it can run around 100 steps. Then, I turned to use SMD method to pull the triple helix along x direction. I tried the following method to generate the box, but got a fatal error. editconf -f complex.gro -o newbox.gro -c -d 1 editconf -f complex.gro -o newbox.gro -center 5.63865 1.8837 1.9762 -box 20 3.8 4.0 ; freeze groups freezegrps = End freezedim = Y Y Y ; COM pulling. pull= umbrella pull-geometry = direction-periodic pull-start = yes pull-ngroups= 2 pull-ncoords= 1 pull-coord1-groups = 1 2 pull-group1-name= End pull-group2-name= pull pull-coord1-rate= 0.01 pull-coord1-k = 1000 pull-coord1-vec = 1 0 0 Fatal error: Can not have dynamic box while using pull geometry 'direction-periodic' (dim x) Could you teach me how can I build a fixed box? And is my SMD code right? This means you can't use pressure coupling in the direction along which you're pulling. Use NVT or align the system such that you are pulling along z, in conjunction with semiisotropic coupling and zero compressibility along z. -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] g_dist
hello everyone I am working on protein complex with popc membrane gromcs version is 4.5.5 i want to calculate the distance between two residues during the simulation (200ns) i have been made the .ndx file of atoms of two residues and concatenate .xtc file and final .tpr file g_dist -f full.xtc -s final.tpr -n atom.ndx -o dist.xvg Molecule in topology has atom numbers below and above natoms (3893). You are probably trying to use a trajectory which does not match the first 3893 atoms of the run input file. You can make a matching run input file with tpbconv. the indx file is having the atom no which are present in last.gro file kindly help g_mindist, g_hbond is working -- 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] A jump in potential just after extension
On 3/16/15 4:45 AM, Faezeh Pousaneh wrote: Hi, I am almost new in Gromacs, I searched about my problem but did not find anything. Can someone please help me? I extend my simulation with same node on same machine, but when I check g_energy I find a sharp jump in potential, why is that so?. (for example if before the extension the average value of potential were X, just as soon as extension starts the average jumps to Y.) my run command: aprun -n 1 tpbconv_mpi -s production.tpr -extend 10 -o production.tpr aprun-n 224 mdrun_mpi -s production.tpr -cpi state.cpt -c production.gro Please post the contents of your original .mdp file. This issue has come up before in very specific cases. Which version of GROMACS are you using? Is it related to http://redmine.gromacs.org/issues/1640 ? -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] A jump in potential just after extension
Dear Justin, I use gromacs/4.6.7. Below is my .mdp file. No that is not similar to my case, I do not change any setting for the extension. (I should add that despite strange jump in potential in g_energy, the trajectory goes in a direction which I expect.) PRODUCTIOn integrator= md dt= 0.002 nsteps= 5000 nstxout = 1 ; save coordinates every ps nstvout = 1 ; save velocities every ps nstlog = 1 ; update log file every nstenergy = 1 ; save energies every nstxtcout= 10 ; Output frequency for xtc file xtc-precision = 10 ; precision for xtc file ns_type = grid; search neighboring grid cells nstlist = 5; fs pbc = xyz ; 3-D PBC rlist = 1.2 ; short-range neighborlist cutoff (in nm) rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm) rvdw = 1.2 ; short-range van der Waals cutoff (in nm) coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing= 0.16; grid spacing for FFT vdw-type= Cut-off Tcoupl= v-rescale ; modified Berendsen thermostat tc-grps = LUT SOL ; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t= 380. 380. ; reference temperature, one for each group, in K ;tc-grps = system energygrps = LUT SOL Pcoupl= Parrinello-Rahman Pcoupltype = Isotropic tau_p = 1.0 compressibility = 4.5e-5 ref_p= 1.0 gen_vel= no gen_temp= 380.0 gen_seed= 712349 DispCorr = EnerPres; account for cut-off vdW scheme constraints = all-bonds ; all bonds constrained (fixed length) continuation = yes ; Restarting after NPT constraint-algorithm = lincs ; holonomic constraints lincs_iter= 1 ; accuracy of LINCS lincs_order= 4 ; also related to accuracy ** Best regards On Mon, Mar 16, 2015 at 12:31 PM, Justin Lemkul jalem...@vt.edu wrote: On 3/16/15 4:45 AM, Faezeh Pousaneh wrote: Hi, I am almost new in Gromacs, I searched about my problem but did not find anything. Can someone please help me? I extend my simulation with same node on same machine, but when I check g_energy I find a sharp jump in potential, why is that so?. (for example if before the extension the average value of potential were X, just as soon as extension starts the average jumps to Y.) my run command: aprun -n 1 tpbconv_mpi -s production.tpr -extend 10 -o production.tpr aprun-n 224 mdrun_mpi -s production.tpr -cpi state.cpt -c production.gro Please post the contents of your original .mdp file. This issue has come up before in very specific cases. Which version of GROMACS are you using? Is it related to http://redmine.gromacs.org/issues/1640 ? -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. -- 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] how to fix the center of mass of the three N-terminal atoms in a triple helix?
Deer all, I am trying to use the steered molecular dynamic method to study a triple helix. According to a paper, it can be done through fixing the COM of the three terminal by means of a strong harmonic restrain with a super large spring constant, and pull the C-terminal by an appropriate spring constant in Gromos96 53a6. But I still do not know how to keep the COM fixed. Could anybody give me same guidance? Thanks a lot, Ming -- 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] Postdoc positions available at IBM (bio-molecular modeling and MD)
Dear all, IBM Thomas J. Watson Research Center located in Yorktown Heights, NY expects to immediately hire three Postdoctoral Fellows in the Soft Matter Science Group, Computational Biology Center. To view the job description and apply, please visit the following link: https://jobs3.netmedia1.com/cp/faces/job_summary?job_id=RES-0731149. For more information, please contact Dr. Payel Das da...@us.ibm.com. -- Payel Das, Ph.D. Research Staff Scientist Soft Matter Theory and Simulations Group Computational Biology Center IBM Thomas J. Watson Research Center Yorktown Heights, NY 10598 Ph:914-945-2373 Webpage: https://researcher.ibm.com/researcher/view.php?person=us-daspa -- 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] Error while shrinking lipids (KALP15 in DPPC tutorial)
Dear gmx-users,
I am repeating the KALP15 in DPPC tutorial using Maximin 3 in DPPC using the
CHARMM36 forcefield. I think the lipid shrinking was a step I did badly last
time (I think I was getting can open em.tpr but not open em1.tpr, em2.tpr,
etc.), which might be why that run had poor lipid packing.
This is the page of the tutorial I am stuck
at:http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/03_solvate.html
The KALP15 in DPPC tutorial says to scale down the lipids by 0.95 for 26 times.
So I repeated this group of 3 commands 26 times:/usr/local/gromacs/bin/gmx
grompp -f minim.mdp -c system_shrink1.gro -p topol.top -o
em.tpr/usr/local/gromacs/bin/gmx mdrun -s em.tpr -vperl inflategro.pl
confout.gro 0.95 DPPC 0 system_shrink1.gro 5 area_shrink1.dat
I am not sure what file to check to make sure doing that is right. I hope it
is.
Anyway I also tried:
cp em.tpr em1.tpr
/usr/local/gromacs/bin/gmx grompp -f minim.mdp -c system_shrink1.gro -p
topol.top -o em1.tpr/usr/local/gromacs/bin/gmx mdrun -s em1.tpr -vperl
inflategro.pl system_shrink1.gro 0.95 DPPC 0 system_shrink2.gro 5
area_shrink2.datcp em1.tpr em2.tpr
/usr/local/gromacs/bin/gmx grompp -f minim.mdp -c system_shrink2.gro -p
topol.top -o em2.tpr/usr/local/gromacs/bin/gmx mdrun -s em2.tpr -vperl
inflategro.pl system_shrink2.gro 0.95 DPPC 0 system_shrink3.gro 5
area_shrink3.datcp em2.tpr em3.tpr
etc.
But then I got this error I have never seen
before:---
Program gmx, VERSION 5.0.1Source code file:
/home/tlipscomb/gromacs-5.0.1/src/gromacs/gmxpreprocess/gmxcpp.c, line: 311
Fatal error:Topology include file gb.itp not foundFor more information and
tips for troubleshooting, please check the GROMACSwebsite at
http://www.gromacs.org/Documentation/Errors---
Line 311 is the contents of this if statement
if (!cpp-fn) { gmx_fatal(FARGS, Topology include file \%s\
not found, filenm); }
Sincerely,Thomas
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Re: [gmx-users] gmx rmsdist: rmsmax vs. rmscmax
Hi, thanks for the reply. I now have another question regarding the the rmsdist tool: I'm confused why my rmsmax value seems so small. Right now I am simulating a box of water only. I'd like to get a matrix of all the atom-atom distances for a single frame in my simulation, so use the following command: gmx rmsdist -f nvt.trr -s nvt.tpr -mean -nosumh -b 100 -e 100 However, this gives an rmsmax = 0.000345129, which is smaller than a water molecule, and Im not sure why. I'm also curious why I need to supply a topology file if all I want to calculate is the interactomic distances. I'm likely misunderstanding this tool... Thanks in advance for the help. Regards, Alan Manning On 03/16/15 04:24, Justin Lemkul wrote: On 3/15/15 6:36 PM, Alan Manning wrote: Hi What is the difference between the rmsmax and rmscmax values written to the screen when running gmx rmsdist? Thanks. rmscmax is scaled by dividing by the mean (sc for scaled, presumably). See calc_rmsd() in gmx_rmsdist.c -Justin -- 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] KALP-15 in DPPC tutorial
check your popc128.top or topol.top file ; Include POPC chain topology #include popc.itp and ; Include water topology #include gromos53a6_lipid.ff/spc.itp and always update the no of atoms in you .gro file On Mon, Mar 16, 2015 at 10:31 AM, RINU KHATTRI nickname.mi...@gmail.com wrote: firstly go back to check your system.gro file which you made bu cat DPPC.gro new_box.gro system.gro remove some line between the merging of two file update the no of atoms then do your next step On Mon, Mar 16, 2015 at 9:38 AM, BAOLIN HUANG baolin.hu...@qut.edu.au wrote: Hi All, I am doing the GROMACS Tutorial of KALP-15 in DPPC. Now, I get stuck at Note how many lipids were deleted and update the [ molecules ] directive of your topology accordingly. Run energy minimization. Then, scale down the lipids by a factor of 0.95 (assuming you have used default names, the result of the minimization is called confout.gro): perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5 area_shrink1.dat The command line was gmx grompp -f minim.mdp -c system_inflated.gro -p topol.top -o em.tpr. And I got Fatal error: number of coordinates in coordinate file (system_inflated.gro, 6438) does not match topology (topol.top 888444) I tried to add DPPC 128 in the [ molecules ], however, I got Fatal error: No such moleculetype DPPC. How to update the [molecules] in topol.top? And how do I know the number of molecules? Kind regards, Alex Huang -- 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] gmx rmsdist: rmsmax vs. rmscmax
On 3/15/15 6:36 PM, Alan Manning wrote: Hi What is the difference between the rmsmax and rmscmax values written to the screen when running gmx rmsdist? Thanks. rmscmax is scaled by dividing by the mean (sc for scaled, presumably). See calc_rmsd() in gmx_rmsdist.c -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] trjconv -center tool
Dear users, i am observing different results for density profile of my system (comprising of hydrated lipids and buffer molecules in aqueous region) if i invoked trjconv tool with and without -center tool. There is difference in the peak height for buffer molecule which are used for centering using -center tool. I will be glad if someone figure out the issue and elaborate on how -center command in trjconv tool works ! -- *Regards,* *Mohammad Sirajuddin.* -- 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] A jump in potential just after extension
Hi, I am almost new in Gromacs, I searched about my problem but did not find anything. Can someone please help me? I extend my simulation with same node on same machine, but when I check g_energy I find a sharp jump in potential, why is that so?. (for example if before the extension the average value of potential were X, just as soon as extension starts the average jumps to Y.) my run command: aprun -n 1 tpbconv_mpi -s production.tpr -extend 10 -o production.tpr aprun-n 224 mdrun_mpi -s production.tpr -cpi state.cpt -c production.gro thank you in advance, Best regards -- 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] problem in defining protonation state of amino acids
Hi Justin, Thanks for your valuable suggestion. I ignored the hydrogen and added manually bu -his flag. Tushar Ranjan Moharana B. Tech, NIT Warangal Ph D Student, CCMB -- 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] Problem in making index.ndx and disres.itp
Hi everyone, I wanted to run a distance restricted MD. Since I have many atoms I can't do it manually with a text editor. For that I choose the line corresponding the atom from .pdb file to another text file and rename them as disres.pdb. Then I run the following command to generate disres.itp *gmx genrestr -f disres.pdb -disre -o disres.itp* I got the following out put Which I don't think correct. Please rectify my mistakes My disres.pdb file ATOM936 CG ASP61 -36.433 1.944 57.629 0.7994 1.700 C ATOM937 OD1 ASP61 -37.626 1.784 58.005 -0.8014 1.500 O ATOM938 OD2 ASP61 -35.856 3.065 57.600 -0.8014 1.500 O ATOM 1212 CD2 HIS81 -41.384 3.133 58.251 -0.1141 1.700 C ATOM 1208 CE1 HIS81 -41.090 2.008 60.045 -0.0170 1.700 C ATOM 1211 HE2 HIS81 -39.455 3.044 59.220 0.3911 1.300 H ATOM 1295 CD2 HIS87 -38.577 6.571 57.666 0.1292 1.700 C ATOM 1292 CE1 HIS87 -39.069 5.316 56.005 0.2057 1.700 C ATOM 1294 NE2 HIS87 -39.012 5.303 57.324 -0.5727 1.550 N ATOM 3657 CG ASP 238 -37.842 3.869 61.472 0.7994 1.700 C ATOM 3658 OD1 ASP 238 -37.982 2.630 61.652 -0.8014 1.500 O ATOM 3659 OD2 ASP 238 -37.595 4.399 60.357 -0.8014 1.500 O END My disres.itp file *; distance restraints for SideChain of [ distance_restraints ]; i j ? label funct loup1up2 weight1 2 1 0 1 0.026104 0.226104 1.2261 11 3 1 1 1 0.0261116 0.2261121.22611 11 4 1 2 1 0.412962 0.6129621.61296 11 5 1 3 1 0.424679 0.6246791.62468 11 6 1 4 1 0.2588 0.4588 1.4588 11 7 1 5 1 0.409973 0.6099731.60997 11 8 1 6 10.357780.557781.55778 11 9 1 7 1 0.324584 0.5245841.52458 1110 1 8 1 0.352323 0.5523231.55232 1111 1 9 1 0.336515 0.5365151.53652 1112 110 1 0.284958 0.4849581.48496 12 3 111 1 0.122214 0.3222141.32221 12 4 112 1 0.300036 0.5000361.50004 12 5 113 10.302630.502631.50263 12 6 114 1 0.153161 0.3531611.35316 12 7 115 1 0.389231 0.5892311.58923 12 8 116 1 0.330781 0.5307811.53078 12 9 117 1 0.284293 0.4842931.48429 1210 118 1 0.305142 0.5051421.50514 1211 119 1 0.276073 0.4760731.47607 1212 120 1 0.251726 0.4517261.45173 13 4 121 1 0.456662 0.6566621.65666 13 5 122 1 0.487282 0.6872821.68728 13 6 123 1 0.294685 0.4946851.49469 13 7 124 10.343850.543851.54385 13 8 125 10.323490.523491.52349 13 9 126 1 0.287881 0.4878811.48788 1310 127 1 0.342527 0.5425271.54253 1311 128 10.359650.559651.55965 1312 129 1 0.252203 0.452203 1.4522 14 5 130 1 0.113787 0.3137871.31379 14 6 131 1 0.116054 0.3160541.31605 14 7 132 1 0.347675 0.5476751.54768 14 8 133 1 0.289477 0.4894771.48948 14 9 134 1 0.234584 0.4345841.43458 1410 135 1 0.384379 0.5843791.58438 1411 136 1 0.383668 0.5836681.58367 1412 137 1 0.351603 0.551603 1.5516 15 6 138 1 0.110408 0.3104081.31041 15 7 139 1 0.472676 0.6726761.67268 15 8 140 1 0.459901 0.659901 1.6599 15 9 141 1 0.375173 0.5751731.57517 1510 142 1 0.300614 0.5006141.50061 1511 143 1 0.255373 0.4553731.45537 1512 144 1 0.324609 0.5246091.52461 16 7 145 1 0.295291 0.4952911.49529
