Fw: [gmx-users] Energy minimization
Sincerely, Shima - Forwarded Message - From: Shima Arasteh shima_arasteh2...@yahoo.com To: Dariush Mohammadyani d.mohammady...@gmail.com Sent: Sunday, December 16, 2012 5:03 PM Subject: Re: [gmx-users] Energy minimization It's printed in terminal, exactly before showing the values of infinite potential and Max Force and . Sincerely, Shima From: Dariush Mohammadyani d.mohammady...@gmail.com To: Shima Arasteh shima_arasteh2...@yahoo.com Sent: Sunday, December 16, 2012 5:01 PM Subject: Re: [gmx-users] Energy minimization Hi Shima, Just for my knowledge, how did you find the clashed atom? Thanks, Dariush On Sun, Dec 16, 2012 at 12:19 AM, Shima Arasteh shima_arasteh2...@yahoo.com wrote: are protein ( atom 288) and lipid chain. I think if I move them, I may get some other clashes, may I not? Any other suggestion? Thanks. -- Dariush Mohammadyani Ph.D Student Department of Bioengineering University of Pittsburgh Pittsburgh, USA -- 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] Energy minimization
It's printed in terminal, exactly before showing the values of infinite potential and Max Force and . Sincerely, Shima From: Dariush Mohammadyani d.mohammady...@gmail.com To: Shima Arasteh shima_arasteh2...@yahoo.com Sent: Sunday, December 16, 2012 5:01 PM Subject: Re: [gmx-users] Energy minimization Hi Shima, Just for my knowledge, how did you find the clashed atom? Thanks, Dariush On Sun, Dec 16, 2012 at 12:19 AM, Shima Arasteh shima_arasteh2...@yahoo.com wrote: are protein ( atom 288) and lipid chain. I think if I move them, I may get some other clashes, may I not? Any other suggestion? Thanks. -- Dariush Mohammadyani Ph.D Student Department of Bioengineering University of Pittsburgh Pittsburgh, USA -- 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] Parametrisation of the cyclic nucleotides in Gromos force fields
On 12/16/12 12:52 AM, James Starlight wrote: Justin, It's not quite understood for me why such errors occurs in the atoms of standard residues when I've bounded them to the C term of my chromophore if the geometry of the adjacent residues might not be changed. So it likely that some errors occur during parametrization of Ignore geometry. Focus on atom types. Bonded interactions are assigned based on what atom types are used for the atoms involved. Their names, coordinates, and all that other stuff are irrelevant for the purposes of pdb2gmx. This email thread has gone on for dozens of messages now, all with basically the same problem - so you need to isolate your focus. It doesn't matter if you're getting two errors or a hundred; work one-by-one to identify each offending interaction type and determine what might be causing it. There's nothing standard about what you're trying to do, and there is no guarantee that there are bonded parameters built-in for the types of interactions you're looking for. In theory, the topology obtained from Swiss-Param should have everything you need in one form or another, such that parameters can be added in, if needed. the molecule which I could not identify ( In any case I'll be very thankful for anyone who can provideme with some other version of the integrated chromophore in charm for my future effort-on-errors :) Surely a search of the literature would turn up people who have simulated GFP using Gromacs, no? Contacting their corresponding author(s) is probably a very efficient means to establishing what others have done. The main problems which I've forced in the improper group definition ( I've not recognize in the paper of simulation in charmm22 what groups should define as improper although Swiss param produce the big set of such groups- see below ) Any planar group (peptide bond, aromatic ring, etc) should be assigned an improper. These are described in the manual. In addition It'll be very hardly to connect chromophore with adjacent residues mainly due to definition of the addition dihedrals. Finally Im not quite sure about CMAP definition ( I've used C NH1 CT1 C NH1 1 24 24\ C NH1 CT1 C N 1 24 24\ in the CMAP.itp with the atom names of chromophore C NH1 CT1 C NC=O 1 24 24\ C NC=O CR C=O N=C 1 24 24\ C=C C=O NC=O CR C=O 1 24 24\ C=O NH1 CT1 C NH1 1 24 24\ where NC=O and N=C types correspond to the N and CR is the C-alpha atoms Again, names are irrelevant. Only the types matter. Note that each CMAP entry corresponds to a huge sequence of numbers (note that '\' is a line continuation character), so I'm not sure what you're trying to do in the cmap.itp file. If deriving CMAP parameters becomes prohibitive, you may need to consider a different force field, though all of the atoms involved should be in the backbone. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Re: Is vacuum simulation NVT?
Could you tell me is there any difference of different Tau_t ussage ( inverse friction in case of Stochastic dynamics) for simulation of water-soluble as well as membrane-proteins ? In the first case I'm using tau_t 2ps that is lower than internal water friction. In the second case one part of protein could be in the membrane ( e.g helixes) but other ( e.g loops) in water media. Both of that solvents have different characteristic viscousity. So what Tau_t should be used in stochastic dynamics for such biphastic systems? I don't think there is a right sd tau_t. You probably want at tau_t^-1 that is lower (tau_t longer) than the natural viscosity of either system, such that the viscosity of the actual intermolecular interactions dominates, not the unphysical viscosity of the thermostat. I don't know how much lower is good enough, though. You may have to experiment. -- 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] Parametrisation of the cyclic nucleotides in Gromos force fields
Justin, thanks again for explanation. So the first 5 atoms in cmap.it correspond to the starting sequence of the backbone atoms of the amino acid doesnt it ? So what is the 24 24 numbers at the end of each cmap line ? E.g in the C NH1 CT1 C NC=O 1 24 24\ the first C B CA C N atoms would be assigned as the backbone. That lines were added after grompp produce error about unknown cmap for that 5 atoms of the chromophore. Should the 24 24 \ be removed from each line of the chromophore cmap ? James -- 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] Parametrisation of the cyclic nucleotides in Gromos force fields
On 12/16/12 10:34 AM, James Starlight wrote: Justin, thanks again for explanation. So the first 5 atoms in cmap.it correspond to the starting sequence of the backbone atoms of the amino acid doesnt it ? So what is the 24 24 numbers at the end of each cmap line ? Probably something related to how Gromacs tools read in the CMAP data. I don't have time to go through the code to find exactly how it's used. E.g in the C NH1 CT1 C NC=O 1 24 24\ the first C B CA C N atoms would be assigned as the backbone. That lines were added after grompp produce error about unknown cmap for that 5 atoms of the chromophore. Should the 24 24 \ be removed from each line of the chromophore cmap ? You shouldn't be modifying anything about cmap.itp, nor should those numbers be present in your .rtp file. Your [cmap] directive in the .rtp entry should contain a sequence of 5 atom names to which the CMAP corrections are applied. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] gold-S simulation
Dear francesco I extract gold parameter from papers that I attached them for you. But for gold and other atom parameters, you should calculate them using common combination rule. Fatemeh Ramezani -- 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] gold-S simulation
hi thanks for your attention, all itp files are in OPLSAA forcefield folder that I attached it for you. Fatemeh Ramezani -- 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] gold-S simulation
Hi fatemeh, thank you for the references. Regarding your problem, what does it means you don't see any interaction? Is it possible it is just a problem of the visualization software. To be sure, you could monitor the distance between any S atom and the Au atom to which it is supposed to be bound. If the distance is stable around the equilibrium value you can say that the interaction is still present Francesco 2012/12/16 fatemeh ramezani fr_...@yahoo.com hi thanks for your attention, all itp files are in OPLSAA forcefield folder that I attached it for you. Fatemeh Ramezani -- 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 -- Cordiali saluti, Dr.Oteri Francesco -- 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] Box Pressure on individual box walls
Hello All, I was wondering if it's possible to get the pressure on individual walls of a pbc cubic box. I specifically want the pressure on the walls perpendicular to the x, y, z axis. Thank you for your time. -- 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] Box Pressure on individual box walls
On 2012-12-16 21:09, John Doe wrote: Hello All, I was wondering if it's possible to get the pressure on individual walls of a pbc cubic box. I specifically want the pressure on the walls perpendicular to the x, y, z axis. g_energy will do it. Thank you for your time. -- 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 -- 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 -- 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] gold-S simulation
On 12/16/12 1:11 PM, francesco oteri wrote: Hi fatemeh, thank you for the references. Regarding your problem, what does it means you don't see any interaction? Is it possible it is just a problem of the visualization software. To be sure, you could monitor the distance between any S atom and the Au atom to which it is supposed to be bound. If the distance is stable around the equilibrium value you can say that the interaction is still present In addition, if one is expecting some sort of covalent association, it must be defined in the topology. This will not be true in the case of protein-Au interactions unless one makes appropriate entries in specbond.dat, similar to heme, or manual addition. Bonded parameters are useless unless there is a bond :) -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Input vdwradii.dat file when using genbox
Dear All, I am practising the tutorial 2 of Gromacs ( KALP-15 in DPPC). In the step Solvate with water,i made a copy of vdwradii.dat and changed the value of C from 0.15 to 0.375. But i don't know how to input this changed file into genbox. I saw genbox -h, and i don't find any option for input file.dat. Thank for any help ! Regards KT -- 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] Input vdwradii.dat file when using genbox
On 12/16/12 10:15 PM, Kieu Thu Nguyen wrote: Dear All, I am practising the tutorial 2 of Gromacs ( KALP-15 in DPPC). In the step Solvate with water,i made a copy of vdwradii.dat and changed the value of C from 0.15 to 0.375. But i don't know how to input this changed file into genbox. I saw genbox -h, and i don't find any option for input file.dat. The file is read automatically. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Input vdwradii.dat file when using genbox
Thank Justin ! But i am not clear Is it read automatically when i put it in the working directory or put it in $GMXLIB ?. The same question with gromos53a6_lipid.ff. To this new forefield, i put it in $GMXLIB as the tutorial said. Regards KT On Mon, Dec 17, 2012 at 10:17 AM, Justin Lemkul jalem...@vt.edu wrote: On 12/16/12 10:15 PM, Kieu Thu Nguyen wrote: Dear All, I am practising the tutorial 2 of Gromacs ( KALP-15 in DPPC). In the step Solvate with water,i made a copy of vdwradii.dat and changed the value of C from 0.15 to 0.375. But i don't know how to input this changed file into genbox. I saw genbox -h, and i don't find any option for input file.dat. The file is read automatically. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- 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] Input vdwradii.dat file when using genbox
I got it. Thank Justin ! Regards KT On Mon, Dec 17, 2012 at 10:28 AM, Kieu Thu Nguyen kieuthu2...@gmail.comwrote: Thank Justin ! But i am not clear Is it read automatically when i put it in the working directory or put it in $GMXLIB ?. The same question with gromos53a6_lipid.ff. To this new forefield, i put it in $GMXLIB as the tutorial said. Regards KT On Mon, Dec 17, 2012 at 10:17 AM, Justin Lemkul jalem...@vt.edu wrote: On 12/16/12 10:15 PM, Kieu Thu Nguyen wrote: Dear All, I am practising the tutorial 2 of Gromacs ( KALP-15 in DPPC). In the step Solvate with water,i made a copy of vdwradii.dat and changed the value of C from 0.15 to 0.375. But i don't know how to input this changed file into genbox. I saw genbox -h, and i don't find any option for input file.dat. The file is read automatically. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- 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] oplsaa force field
Sir, I studying the dynamics of membrane proteins.First I did a 20 ns simulation using GROMOS96 53a6.This force field cause some problems in the helical part of the protein.Now I am trying to do the same simulation with opls-aa force field.Is the changes I should have to do in ffnonbonded.itp and ffbonded,itp is same as in the justin manual? -- 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
