[gmx-users] restrain COM of a group of atoms
Dear Gromacs experts and users, I am here to seek help. I want to use constraint pull method to pull a filament. My plan is to keep the center of mass of one group fixed through a stiff restraint, say 3×10e5, and pull the other group. I tried to generate the restraint .itp file and modify the topol ifle, but found that I can only restrain all of the atoms, not the COM of the group. There are 2 journals, in which the authors said they used this method like this: To apply uniaxial tension, the center of mass of the N-terminal C − α atoms of the two chains was fixed by a stiff harmonic spring and referred as the reference group. they used GROMACS 4.6. I am using version 5.0.4. I tried to use pull code to achieve this, but failed. My code is like this: pull= constraint pull-geometry = direction-periodic pull-start = yes pull-ngroups= 2 pull-ncoords= 2 pull-coord1-groups = 1 pull-coord2-groups = 2 pull-group1-name= G1 pull-group2-name= G2 pull-coord1-rate= 0.0005 pull-coord2-rate= 0 pull-coord1-k = 4000 pull-coord2-k = 30 pull-coord1-vec = 1 0 0 pull-coord2-vec = 1 0 0 using this pull code, I found that only the displacement along Z direction of COM of G1 was 0 during the simulation, and the displacement along both x direction and y direction changed. Could anybody give me some guidance? Thanks. -- 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] on trjcat command
Dear All, The command trjcat can be used for connection of trr files and xtc files in the similar manner, and suppose the first MD is from 0 to 1 ns, the second MD is from 1 ns to 4 ns, the third MD is from 4 ns to 4.5 ns, by trjcat we can get the whole trr file from 0 nx to 4.5 ns, and if the input is the xtc files, we can then get the whole xtc file from 0 nx to 4.5 ns, am I right? Brett -- 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] pdb2gmx error
Dear Users I am trying to run pdb2gmx (in gromacs 5.0.5 and by 43a1p.ff) on o modeled structure holding ATP, water and TPO as hetero atoms. but I am faced with the following error. I checked all LUE residues (although I have got no residue with 28215089 number) and I found no missing atom N. I am really wondering what should be my next step. could you help me on this? Fatal error:Residue 28215089 named LEU of a molecule in the input file was mapped to an entry in the topology database, but the atom N used in an interaction of type improper in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. Best regardsSaman -- 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] on trjcat command
Right. Note that trjcat can also convert the file format. Cheers, Tsjerk On Jul 5, 2015 9:32 AM, Brett brettliu...@163.com wrote: Dear All, The command trjcat can be used for connection of trr files and xtc files in the similar manner, and suppose the first MD is from 0 to 1 ns, the second MD is from 1 ns to 4 ns, the third MD is from 4 ns to 4.5 ns, by trjcat we can get the whole trr file from 0 nx to 4.5 ns, and if the input is the xtc files, we can then get the whole xtc file from 0 nx to 4.5 ns, am I right? Brett -- 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] Why is there a difference between an angle of 0 or 180 deg. for a type 9 proper dihedral with multiplicity of 2?
On 7/5/15 12:56 AM, Christopher Neale wrote: Dear Justin: Thank you for your help. I am glad to see that I was not way out to lunch in my interpretation of multiplicity and proper dihedral angles. First, the out-of-plane motions are not minor. Even just in EM, the dihedral angles along the main ring convert from near 0 deg to about 50 deg, so I think that we're into the neighbourhood of major problems here. Second, my test system was a single ring, like benzene but with a couple of substituents. However, I can reproduce this issue in a standard molecule as follows, so I do not think that the issue has anything to do with my exotic molecule. Take any peptide/protein with a phenylalanine. There are 24 proper dihedral angles around the PHE sidechain ring in the amber99 force field. In this force field, these dihedral angles are all 180 deg / Fc=15.1669998 / mult=2. I take my toplogy out of pdb2gmx and specify these parameters in the .top file and run EM and I still get the planar ring, as expected. Now I simply change those N=24 occurrences of 180 deg to 0 deg (still multiplicity=2) and I run EM and I get these ~50 deg dihedral angles around the ring. This is still wit! h g romacs 4.6.3. I have not checked with other versions of gromacs. If you make a PHE-PHE peptide in VMD with molefacture (2 aa's to avoid the problem amber has with a single amino acid and the termini), then run it through pdb2gmx (v. 4.6.3) the lines in the [ dihedrals ] section that need modification to adjust the proper dihedral angles in the ring of the first PHE sidechain are: 7101112 9 0 15.1669998 2 7101113 9 0 15.1669998 2 19101112 9 0 15.1669998 2 19101113 9 0 15.1669998 2 7101917 9 0 15.1669998 2 7101920 9 0 15.1669998 2 11101917 9 0 15.1669998 2 11101920 9 0 15.1669998 2 10111314 9 0 15.1669998 2 10111315 9 0 15.1669998 2 12111314 9 0 15.1669998 2 12111315 9 0 15.1669998 2 11131516 9 0 15.1669998 2 11131517 9 0 15.1669998 2 14131516 9 0 15.1669998 2 14131517 9 0 15.1669998 2 13151718 9 0 15.1669998 2 13151719 9 0 15.1669998 2 16151718 9 0 15.1669998 2 16151719 9 0 15.1669998 2 15171910 9 0 15.1669998 2 15171920 9 0 15.1669998 2 18171910 9 0 15.1669998 2 18171920 9 0 15.1669998 2 Can you send the full topology, or at least the [atoms] section? I can't decipher what these actually should be. -Justin where I get the bizarre conformations when I use the above, but if I switch the 0's to 180's (recovering the original force field) then I get a planar ring. Therefore, I think that either I am misunderstanding something about proper dihedrals and multiplicity = 2 or there is a more serious problem. What I don't understand at this point is that the force fields (amber at least) actually contain quite a few proper dihedrals that do use angle = 0 and multiplicity = 2, so what is special aboutthe PHE test case outlined above that leads them to not work whereas they are obviously intended to work. I'll take a look into other gromacs versions when I have a chance and will report back. Thank you, Chris. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Justin Lemkul jalem...@vt.edu Sent: 04 July 2015 09:41 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Why is there a difference between an angle of 0 or 180 deg. for a type 9 proper dihedral with multiplicity of 2? On 7/4/15 3:32 AM, Christopher Neale wrote: Dear Gromacs users: I have been working on creating a topology for an exotic molecule. It contains aromatic rings and my parameters always seemed to allow the rings to buckle and become non-planer, much like a glucose ring would (though a little less extensively). However, I have managed to solve the problem by switching my proper (type 9) dihedral angles from angle = 0 degrees, multiplicity = 2 to angle = 180 degrees, multiplicity = 2. I thought that those two conditions should be equivalent and it was only by seriously simplifying the molecule down to a single ring and then toying with every conceivable parameter that I even hit on this. I am using gromacs 4.6.3 and have not tried other versions of gromacs, but this makes so little sense to me that I thought I would ask about it here. There are lots of proper dihedrals in the available force fields that use dihedrals with a set angle of zero degrees,
[gmx-users] g_clustsize
g_clustsize creates file 'histo-clust.xvg'. What does y-axis in this file mean? If this is a probability than of what? @title Cluster size distribution @xaxis label Cluster size @yaxis label () @TYPE xy 0 0.000 128.385 2 7.135 3 1.552 4 0.447 5 0.120 6 0.034 7 0.009 8 0.003 9 0.001 10 0.000 11 0.000 12 0.000 -- 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] Why is there a difference between an angle of 0 or 180 deg. for a type 9 proper dihedral with multiplicity of 2?
Dear Justin: here is a topology followed by initial coordinates (in which the rings of both Phe are planar, straight out of molefacture/pdb2gmx). Run this in EM or MD and the SC ring of Phe #1 will distort. However, replace 0 15.1669998 2 by 180 15.1669998 2 and everything is groovy. Chris. ### ### TOPOLOGY ; ; File 'topol.top' was generated ; By user: lh824914 (36108) ; On host: headnode.rit.albany.edu ; At date: Sat Jul 4 23:10:10 2015 ; ; This is a standalone topology file ; ; It was generated using program: ; pdb2gmx - VERSION 4.6.3 ; ; Command line was: ; pdb2gmx -f FF.gro -ignh ; ; Force field was read from the standard Gromacs share directory. ; ; Include forcefield parameters #include amber99.ff/forcefield.itp [ moleculetype ] ; Namenrexcl Protein 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB ; residue 1 PHE rtp NPHE q +1.0 1 N3 1PHE N 1 0.1737 14.01 ; qtot 0.1737 2 H 1PHE H1 2 0.1921 1.008 ; qtot 0.3658 3 H 1PHE H2 3 0.1921 1.008 ; qtot 0.5579 4 H 1PHE H3 4 0.1921 1.008 ; qtot 0.75 5 CT 1PHE CA 5 0.0733 12.01 ; qtot 0.8233 6 HP 1PHE HA 6 0.1041 1.008 ; qtot 0.9274 7 CT 1PHE CB 7 0.033 12.01 ; qtot 0.9604 8 HC 1PHEHB1 8 0.0104 1.008 ; qtot 0.9708 9 HC 1PHEHB2 9 0.0104 1.008 ; qtot 0.9812 10 CA 1PHE CG 10 0.0031 12.01 ; qtot 0.9843 11 CA 1PHECD1 11-0.1392 12.01 ; qtot 0.8451 12 HA 1PHEHD1 12 0.1374 1.008 ; qtot 0.9825 13 CA 1PHECE1 13-0.1602 12.01 ; qtot 0.8223 14 HA 1PHEHE1 14 0.1433 1.008 ; qtot 0.9656 15 CA 1PHE CZ 15-0.1208 12.01 ; qtot 0.8448 16 HA 1PHE HZ 16 0.1329 1.008 ; qtot 0.9777 17 CA 1PHECE2 17-0.1603 12.01 ; qtot 0.8174 18 HA 1PHEHE2 18 0.1433 1.008 ; qtot 0.9607 19 CA 1PHECD2 19-0.1391 12.01 ; qtot 0.8216 20 HA 1PHEHD2 20 0.1374 1.008 ; qtot 0.959 21 C 1PHE C 21 0.6123 12.01 ; qtot 1.571 22 O 1PHE O 22-0.5713 16 ; qtot 1 ; residue 2 PHE rtp CPHE q -1.0 23 N 2PHE N 23-0.3821 14.01 ; qtot 0.6179 24 H 2PHE H 24 0.2681 1.008 ; qtot 0.886 25 CT 2PHE CA 25-0.1825 12.01 ; qtot 0.7035 26 H1 2PHE HA 26 0.1098 1.008 ; qtot 0.8133 27 CT 2PHE CB 27-0.0959 12.01 ; qtot 0.7174 28 HC 2PHEHB1 28 0.0443 1.008 ; qtot 0.7617 29 HC 2PHEHB2 29 0.0443 1.008 ; qtot 0.806 30 CA 2PHE CG 30 0.0552 12.01 ; qtot 0.8612 31 CA 2PHECD1 31 -0.13 12.01 ; qtot 0.7312 32 HA 2PHEHD1 32 0.1408 1.008 ; qtot 0.872 33 CA 2PHECE1 33-0.1847 12.01 ; qtot 0.6873 34 HA 2PHEHE1 34 0.1461 1.008 ; qtot 0.8334 35 CA 2PHE CZ 35-0.0944 12.01 ; qtot 0.739 36 HA 2PHE HZ 36 0.128 1.008 ; qtot 0.867 37 CA 2PHECE2 37-0.1847 12.01 ; qtot 0.6823 38 HA 2PHEHE2 38 0.1461 1.008 ; qtot 0.8284 39 CA 2PHECD2 39 -0.13 12.01 ; qtot 0.6984 40 HA 2PHEHD2 40 0.1408 1.008 ; qtot 0.8392 41 C 2PHE C 41 0.766 12.01 ; qtot 1.605 42 O2 2PHEOC1 42-0.8026 16 ; qtot 0.8026 43 O2 2PHEOC2 43-0.8026 16 ; qtot 0 [ bonds ] ; aiaj functc0c1c2c3 1 2 1 1 3 1 1 4 1 1 5 1 5 6 1 5 7 1 521 1 7 8 1 7 9 1 710 1 1011 1
Re: [gmx-users] restrain COM of a group of atoms
I do now know what authors meant. However, the COM-COM pulling implies that one group is restrained and another group moves relative to it. So, the COM of the reference group is already fixed in the pull code. On Sun, Jul 5, 2015 at 4:02 AM, Ming Tang qut20181...@gmail.com wrote: Dear Gromacs experts and users, I am here to seek help. I want to use constraint pull method to pull a filament. My plan is to keep the center of mass of one group fixed through a stiff restraint, say 3×10e5, and pull the other group. I tried to generate the restraint .itp file and modify the topol ifle, but found that I can only restrain all of the atoms, not the COM of the group. There are 2 journals, in which the authors said they used this method like this: To apply uniaxial tension, the center of mass of the N-terminal C − α atoms of the two chains was fixed by a stiff harmonic spring and referred as the reference group. they used GROMACS 4.6. I am using version 5.0.4. I tried to use pull code to achieve this, but failed. My code is like this: pull= constraint pull-geometry = direction-periodic pull-start = yes pull-ngroups= 2 pull-ncoords= 2 pull-coord1-groups = 1 pull-coord2-groups = 2 pull-group1-name= G1 pull-group2-name= G2 pull-coord1-rate= 0.0005 pull-coord2-rate= 0 pull-coord1-k = 4000 pull-coord2-k = 30 pull-coord1-vec = 1 0 0 pull-coord2-vec = 1 0 0 using this pull code, I found that only the displacement along Z direction of COM of G1 was 0 during the simulation, and the displacement along both x direction and y direction changed. Could anybody give me some guidance? Thanks. -- 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] Why is there a difference between an angle of 0 or 180 deg. for a type 9 proper dihedral with multiplicity of 2?
On 7/5/15 9:10 AM, Christopher Neale wrote: Dear Justin: here is a topology followed by initial coordinates (in which the rings of both Phe are planar, straight out of molefacture/pdb2gmx). Run this in EM or MD and the SC ring of Phe #1 will distort. However, replace 0 15.1669998 2 by 180 15.1669998 2 and everything is groovy. My initial gut reaction (and yours) was incorrect. Plot the cosine series of 15.167(1-cos(2*phi-180) vs. 15.167(1-cos(2*phi)) and you will see that the minima that you obtain when the phase is 180 have become maxima. Hence when you switch the phase angle between 0 and 180, you completely invert the energy landscape. Really wild to watch a planar benzene convert to a chair, pseudo-cyclohexane :) -Justin Chris. ### ### TOPOLOGY ; ; File 'topol.top' was generated ; By user: lh824914 (36108) ; On host: headnode.rit.albany.edu ; At date: Sat Jul 4 23:10:10 2015 ; ; This is a standalone topology file ; ; It was generated using program: ; pdb2gmx - VERSION 4.6.3 ; ; Command line was: ; pdb2gmx -f FF.gro -ignh ; ; Force field was read from the standard Gromacs share directory. ; ; Include forcefield parameters #include amber99.ff/forcefield.itp [ moleculetype ] ; Namenrexcl Protein 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB ; residue 1 PHE rtp NPHE q +1.0 1 N3 1PHE N 1 0.1737 14.01 ; qtot 0.1737 2 H 1PHE H1 2 0.1921 1.008 ; qtot 0.3658 3 H 1PHE H2 3 0.1921 1.008 ; qtot 0.5579 4 H 1PHE H3 4 0.1921 1.008 ; qtot 0.75 5 CT 1PHE CA 5 0.0733 12.01 ; qtot 0.8233 6 HP 1PHE HA 6 0.1041 1.008 ; qtot 0.9274 7 CT 1PHE CB 7 0.033 12.01 ; qtot 0.9604 8 HC 1PHEHB1 8 0.0104 1.008 ; qtot 0.9708 9 HC 1PHEHB2 9 0.0104 1.008 ; qtot 0.9812 10 CA 1PHE CG 10 0.0031 12.01 ; qtot 0.9843 11 CA 1PHECD1 11-0.1392 12.01 ; qtot 0.8451 12 HA 1PHEHD1 12 0.1374 1.008 ; qtot 0.9825 13 CA 1PHECE1 13-0.1602 12.01 ; qtot 0.8223 14 HA 1PHEHE1 14 0.1433 1.008 ; qtot 0.9656 15 CA 1PHE CZ 15-0.1208 12.01 ; qtot 0.8448 16 HA 1PHE HZ 16 0.1329 1.008 ; qtot 0.9777 17 CA 1PHECE2 17-0.1603 12.01 ; qtot 0.8174 18 HA 1PHEHE2 18 0.1433 1.008 ; qtot 0.9607 19 CA 1PHECD2 19-0.1391 12.01 ; qtot 0.8216 20 HA 1PHEHD2 20 0.1374 1.008 ; qtot 0.959 21 C 1PHE C 21 0.6123 12.01 ; qtot 1.571 22 O 1PHE O 22-0.5713 16 ; qtot 1 ; residue 2 PHE rtp CPHE q -1.0 23 N 2PHE N 23-0.3821 14.01 ; qtot 0.6179 24 H 2PHE H 24 0.2681 1.008 ; qtot 0.886 25 CT 2PHE CA 25-0.1825 12.01 ; qtot 0.7035 26 H1 2PHE HA 26 0.1098 1.008 ; qtot 0.8133 27 CT 2PHE CB 27-0.0959 12.01 ; qtot 0.7174 28 HC 2PHEHB1 28 0.0443 1.008 ; qtot 0.7617 29 HC 2PHEHB2 29 0.0443 1.008 ; qtot 0.806 30 CA 2PHE CG 30 0.0552 12.01 ; qtot 0.8612 31 CA 2PHECD1 31 -0.13 12.01 ; qtot 0.7312 32 HA 2PHEHD1 32 0.1408 1.008 ; qtot 0.872 33 CA 2PHECE1 33-0.1847 12.01 ; qtot 0.6873 34 HA 2PHEHE1 34 0.1461 1.008 ; qtot 0.8334 35 CA 2PHE CZ 35-0.0944 12.01 ; qtot 0.739 36 HA 2PHE HZ 36 0.128 1.008 ; qtot 0.867 37 CA 2PHECE2 37-0.1847 12.01 ; qtot 0.6823 38 HA 2PHEHE2 38 0.1461 1.008 ; qtot 0.8284 39 CA 2PHECD2 39 -0.13 12.01 ; qtot 0.6984 40 HA 2PHEHD2 40 0.1408 1.008 ; qtot 0.8392 41 C
Re: [gmx-users] g_clustsize
On 05/07/15 14:09, V.V.Chaban wrote: g_clustsize creates file 'histo-clust.xvg'. What does y-axis in this file mean? If this is a probability than of what? Probability of cluster size, what else? @title Cluster size distribution @xaxis label Cluster size @yaxis label () @TYPE xy 0 0.000 128.385 2 7.135 3 1.552 4 0.447 5 0.120 6 0.034 7 0.009 8 0.003 9 0.001 10 0.000 11 0.000 12 0.000 -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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] Why is there a difference between an angle of 0 or 180 deg. for a type 9 proper dihedral with multiplicity of 2?
I see, thank you Justin. I guess that even though I did read the equation, which is: K(1 + cos(n*phi - phi_s) I was actually thinking: K(1 + cos(n* [ phi - phi_s ] ) so everything is as it should be. Thanks for all your help, Chris. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Justin Lemkul jalem...@vt.edu Sent: 05 July 2015 13:12 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Why is there a difference between an angle of 0 or 180 deg. for a type 9 proper dihedral with multiplicity of 2? On 7/5/15 9:10 AM, Christopher Neale wrote: Dear Justin: here is a topology followed by initial coordinates (in which the rings of both Phe are planar, straight out of molefacture/pdb2gmx). Run this in EM or MD and the SC ring of Phe #1 will distort. However, replace 0 15.1669998 2 by 180 15.1669998 2 and everything is groovy. My initial gut reaction (and yours) was incorrect. Plot the cosine series of 15.167(1-cos(2*phi-180) vs. 15.167(1-cos(2*phi)) and you will see that the minima that you obtain when the phase is 180 have become maxima. Hence when you switch the phase angle between 0 and 180, you completely invert the energy landscape. Really wild to watch a planar benzene convert to a chair, pseudo-cyclohexane :) -Justin Chris. ### ### TOPOLOGY ; ; File 'topol.top' was generated ; By user: lh824914 (36108) ; On host: headnode.rit.albany.edu ; At date: Sat Jul 4 23:10:10 2015 ; ; This is a standalone topology file ; ; It was generated using program: ; pdb2gmx - VERSION 4.6.3 ; ; Command line was: ; pdb2gmx -f FF.gro -ignh ; ; Force field was read from the standard Gromacs share directory. ; ; Include forcefield parameters #include amber99.ff/forcefield.itp [ moleculetype ] ; Namenrexcl Protein 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB ; residue 1 PHE rtp NPHE q +1.0 1 N3 1PHE N 1 0.1737 14.01 ; qtot 0.1737 2 H 1PHE H1 2 0.1921 1.008 ; qtot 0.3658 3 H 1PHE H2 3 0.1921 1.008 ; qtot 0.5579 4 H 1PHE H3 4 0.1921 1.008 ; qtot 0.75 5 CT 1PHE CA 5 0.0733 12.01 ; qtot 0.8233 6 HP 1PHE HA 6 0.1041 1.008 ; qtot 0.9274 7 CT 1PHE CB 7 0.033 12.01 ; qtot 0.9604 8 HC 1PHEHB1 8 0.0104 1.008 ; qtot 0.9708 9 HC 1PHEHB2 9 0.0104 1.008 ; qtot 0.9812 10 CA 1PHE CG 10 0.0031 12.01 ; qtot 0.9843 11 CA 1PHECD1 11-0.1392 12.01 ; qtot 0.8451 12 HA 1PHEHD1 12 0.1374 1.008 ; qtot 0.9825 13 CA 1PHECE1 13-0.1602 12.01 ; qtot 0.8223 14 HA 1PHEHE1 14 0.1433 1.008 ; qtot 0.9656 15 CA 1PHE CZ 15-0.1208 12.01 ; qtot 0.8448 16 HA 1PHE HZ 16 0.1329 1.008 ; qtot 0.9777 17 CA 1PHECE2 17-0.1603 12.01 ; qtot 0.8174 18 HA 1PHEHE2 18 0.1433 1.008 ; qtot 0.9607 19 CA 1PHECD2 19-0.1391 12.01 ; qtot 0.8216 20 HA 1PHEHD2 20 0.1374 1.008 ; qtot 0.959 21 C 1PHE C 21 0.6123 12.01 ; qtot 1.571 22 O 1PHE O 22-0.5713 16 ; qtot 1 ; residue 2 PHE rtp CPHE q -1.0 23 N 2PHE N 23-0.3821 14.01 ; qtot 0.6179 24 H 2PHE H 24 0.2681 1.008 ; qtot 0.886 25 CT 2PHE CA 25-0.1825 12.01 ; qtot 0.7035 26 H1 2PHE HA 26 0.1098 1.008 ; qtot 0.8133 27 CT 2PHE CB 27-0.0959 12.01 ; qtot 0.7174 28 HC 2PHEHB1 28 0.0443 1.008 ; qtot 0.7617 29 HC 2PHEHB2 29 0.0443 1.008 ; qtot 0.806 30 CA 2PHE CG 30 0.0552 12.01 ; qtot 0.8612 31 CA 2PHECD1 31 -0.13 12.01 ; qtot 0.7312 32 HA 2PHEHD1 32 0.1408 1.008 ; qtot 0.872
Re: [gmx-users] g_clustsize
The sum of these probabilities is never the same. It is confusing. If no clusters exist (all particles are lone) then the sum of probabilities equals the sum of all particles. If clusters exist, the sum is different and it is unclear how it is derived. If the output property is still a probability: is it a probability that N atoms exist as a cluster or it is a probability that such a cluster exists within all possible clusters (a fraction of a given cluster)? On Sun, Jul 5, 2015 at 5:40 PM, David van der Spoel sp...@xray.bmc.uu.se wrote: On 05/07/15 14:09, V.V.Chaban wrote: g_clustsize creates file 'histo-clust.xvg'. What does y-axis in this file mean? If this is a probability than of what? Probability of cluster size, what else? @title Cluster size distribution @xaxis label Cluster size @yaxis label () @TYPE xy 0 0.000 128.385 2 7.135 3 1.552 4 0.447 5 0.120 6 0.034 7 0.009 8 0.003 9 0.001 10 0.000 11 0.000 12 0.000 -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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.
