[gmx-users] Density of the box
Thank you Tsjerk! Actually I was not using any dummy atoms or united atoms in this case. I was using a pdb file with just water atoms (1BP2). Kindly excuse me I was not recieving any replys to my mail id ka...@rishi.serc.iisc.ernet.in. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Density of the box
Dear Gromacs users, I was trying to run a simulation using a protein of 123 aa long and wanted to adjust the density to 993.04g/l so with the following command I ran the editconf: editconf -f conf.pdb -o box.pdb -bt cubic -d 0.8 -density 997.0479 Its output was as follows: -- . . Read 1842 atoms Volume: 115.734 nm^3, corresponds to roughly 52000 electrons No velocities found system size : 3.370 4.749 4.270 (nm) diameter: 4.979 (nm) center : 1.646 1.395 2.422 (nm) box vectors : 4.707 6.445 3.815 (nm) box angles : 90.00 90.00 90.00 (degrees) box volume : 115.73 (nm^3) Volume of input 115.734 (nm^3) Massof input 42476.2 (a.m.u.) Density of input 609.444 (g/l) Scaling all box vectors by 0.848671 new system size : 2.860 4.030 3.624 shift : 1.893 2.106 1.234 (nm) new center : 3.289 3.289 3.289 (nm) new box vectors : 6.579 6.579 6.579 (nm) new box angles : 90.00 90.00 90.00 (degrees) new box volume : 284.70 (nm^3) --- My doubt here is it says that the Mass of input is 42476.2 (a.m.u.), but the mass of protein is 13795.4 Da (according to the protparam with sequence input). I am not sure whether protparam takes into account hydrogens. Even with the inclusion of hydrogens (885), the molecular weight will still be 14686.49Da. So how is 42476.2 a.m.u. comes? Thank you all in advance MKS -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Density of the box
On 10/01/2011 7:59 PM, ka...@rishi.serc.iisc.ernet.in wrote: Dear Gromacs users, I was trying to run a simulation using a protein of 123 aa long and wanted to adjust the density to 993.04g/l so with the following command I ran the editconf: editconf -f conf.pdb -o box.pdb -bt cubic -d 0.8 -density 997.0479 Its output was as follows: -- . . Read 1842 atoms Volume: 115.734 nm^3, corresponds to roughly 52000 electrons No velocities found system size : 3.370 4.749 4.270 (nm) diameter: 4.979 (nm) center : 1.646 1.395 2.422 (nm) box vectors : 4.707 6.445 3.815 (nm) box angles : 90.00 90.00 90.00 (degrees) box volume : 115.73 (nm^3) Volume of input 115.734 (nm^3) Massof input 42476.2 (a.m.u.) Density of input 609.444 (g/l) Scaling all box vectors by 0.848671 new system size : 2.860 4.030 3.624 shift : 1.893 2.106 1.234 (nm) new center : 3.289 3.289 3.289 (nm) new box vectors : 6.579 6.579 6.579 (nm) new box angles : 90.00 90.00 90.00 (degrees) new box volume : 284.70 (nm^3) --- My doubt here is it says that the Mass of input is 42476.2 (a.m.u.), but the mass of protein is 13795.4 Da (according to the protparam with sequence input). I am not sure whether protparam takes into account hydrogens. Even with the inclusion of hydrogens (885), the molecular weight will still be 14686.49Da. So how is 42476.2 a.m.u. comes? Hmm, that's the second post in a week reporting editconf giving an apparently spurious measurement of the mass. Sounds like it could be a bug. Thoughts, anyone? Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Density of the box
Sir, I am using Gromacs 4.0.7 version. Does this problem exits in other older or newer versions? what is the density of water that spc216 adds? If it is a fixed density, then i encountered a problem - I tried using 1 water molecule as a system (instead of protein), in a cubic box with 0.8nm distance (-d), and filled it with spc216 water, in this case the density it showed was 933.221g/l, Output configuration contains 513 atoms in 171 residues Volume : 5.48157 (nm^3) Density: 933.221 (g/l) Number of SOL molecules:171 - but when I used the same system i.e water, with a cubic box of 1.0nm distact from water (-d) and filled with spc216 water it gave a density of 1001.85g/l, -- Output configuration contains 1017 atoms in 339 residues Volume : 10.1226 (nm^3) Density: 1001.85 (g/l) Number of SOL molecules:339 -- So does this trend indicate that the density increases with increase in volume of the same system? and spc216 does not add water according to a specific density? With Regards MKS Hmm, that's the second post in a week reporting editconf giving an apparently spurious measurement of the mass. Sounds like it could be a bug. Thoughts, anyone? Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Density of the box
Hi, editconf needs to take the masses from a database file if not fed with a run input file. It will probably miss out on some types of atoms or get the masses wrong, especially with united atoms and/or dummies. Probably the density would be correct giving a .tpr file for input. Cheers, Tsjerk On Mon, Jan 10, 2011 at 4:06 PM, ka...@rishi.serc.iisc.ernet.in wrote: Sir, I am using Gromacs 4.0.7 version. Does this problem exits in other older or newer versions? what is the density of water that spc216 adds? If it is a fixed density, then i encountered a problem - I tried using 1 water molecule as a system (instead of protein), in a cubic box with 0.8nm distance (-d), and filled it with spc216 water, in this case the density it showed was 933.221g/l, Output configuration contains 513 atoms in 171 residues Volume : 5.48157 (nm^3) Density : 933.221 (g/l) Number of SOL molecules: 171 - but when I used the same system i.e water, with a cubic box of 1.0nm distact from water (-d) and filled with spc216 water it gave a density of 1001.85g/l, -- Output configuration contains 1017 atoms in 339 residues Volume : 10.1226 (nm^3) Density : 1001.85 (g/l) Number of SOL molecules: 339 -- So does this trend indicate that the density increases with increase in volume of the same system? and spc216 does not add water according to a specific density? With Regards MKS Hmm, that's the second post in a week reporting editconf giving an apparently spurious measurement of the mass. Sounds like it could be a bug. Thoughts, anyone? Mark -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
