[gmx-users] Re: Dielectric constant calculation with Gromacs-3.3.1
Hi David~ Thanks for your quick reply. Just want to make sure, the inf in the following message you posted before means setting epsilon_surface to be 0 (default value) in mdp file? Thanks again! - Liang http://lists.gromacs.org/pipermail/gmx-users/2002-March/001089.html -- View this message in context: http://gromacs.5086.n6.nabble.com/Dielectric-constant-calculation-with-Gromacs-3-3-1-tp4563288p4563352.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] Dielectric constant calculation with Gromacs-3.3.1
Hi~ I am going to calculate the dielectric constant of rigid water model, but I am not quite sure about the use of boundary condition. I know there is an option "epsilon_surface", and its default number is 0. I am using PME to calculate electrostatic interaction. From the literature and the mailing list, it seems there are 2 following options: 1. set epsilon_surface to be its default value 0, and use g_dipoles to calculate the dielectric constant. 2. set epsilon_surface to be inf (someone calls this conducting boundary condition), and use g_dipoles to calculate the dielectric constant. Here I am not sure which option I should use. epsilon_RF seems just to work with reaction field method, not PME. But I don't see any option for PME. And I am not sure what formula is used for the dielectric constant in Gromacs: Let a = (4*pi*) / (3*k*T*V) in Gaussian unit assuming =0 For case 1: it seems to be: epsilon = 1/(1-a) For case 2: it seems to be: epsilon = 1+a And finally I think these two cases (epsilon_surface in MD and corresponding formula) should give very close answer. But I am not sure which way is better. Could any one please help me sort this out? And I am using Gromacs-3.3.1. Thanks, Liang -- 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] Limit on energygrp_table
While, is it needed to list all the possible interacting (two) atoms in the energygrp_table option? I have more than 3000 possible two-atom pairs, corresponding to more than 3000 table_*.xvg files. On Wed, Nov 30, 2011 at 12:29 AM, Mark Abraham wrote: > On 30/11/2011 5:25 PM, Liu, Liang wrote: > > The error shows as "An input file contains a line longer than 4095 > characters, while the buffer passed to fgets2 has size 4095." > > > No text table file needs a line this long. We still don't have information > from you, but I expect you have a malformed file. > > Mark > > > > On Wed, Nov 30, 2011 at 12:22 AM, Mark Abraham > wrote: > >> On 30/11/2011 5:09 PM, Liu, Liang wrote: >> >> Dear all, >> >> I am trying to use tabulated potentials in my simulation. However, >> there is a limit on energygrp_table and the grompp reports error. >> >> >> What error? >> >> >> The interaction happens between any two of atoms, and their might be >> more than 3000 possible couples. >> What should I do to remove the limit? Thanks. >> >> >> We don't know what limit you are observing. >> >> 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 >> > > > > -- > Best, > Liang Liu > > > > > -- > 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 > -- Best, Liang Liu -- 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] Limit on energygrp_table
The error shows as "An input file contains a line longer than 4095 characters, while the buffer passed to fgets2 has size 4095." On Wed, Nov 30, 2011 at 12:22 AM, Mark Abraham wrote: > On 30/11/2011 5:09 PM, Liu, Liang wrote: > > Dear all, > > I am trying to use tabulated potentials in my simulation. However, there > is a limit on energygrp_table and the grompp reports error. > > > What error? > > > The interaction happens between any two of atoms, and their might be > more than 3000 possible couples. > What should I do to remove the limit? Thanks. > > > We don't know what limit you are observing. > > 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 > -- Best, Liang Liu -- 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] Limit on energygrp_table
Dear all, I am trying to use tabulated potentials in my simulation. However, there is a limit on energygrp_table and the grompp reports error. The interaction happens between any two of atoms, and their might be more than 3000 possible couples. What should I do to remove the limit? Thanks. -- Best, Liang Liu -- 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] what's the math algorithm?
Dear all, Assuming I have a some tabulated potentials, table.xvg, tablep.xvg, table_P_P.xvg, table_P_C.xvg and so on. Also there are non-zero values in the first column of both table.xvg and tablep.xvg; while the first column (x), the six column (h(x)) and the last column (h'(x)) have non-zero numbers. All other columns have only 0. So what's the math behind it? Thanks. -- Best, Liang Liu -- 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] calculate potential with tabulated non-bonded interactions
Well my first question is: if the pdb2gmx command must take a force file? I guess it should be necessary. Then the available list contains amber and others, but not user-specified potential. This will affect the future simulation or calculation? On Thu, Nov 17, 2011 at 10:06 AM, Justin A. Lemkul wrote: > > > Liu, Liang wrote: > >> Well, I already have the xvg files from others. However I don't know how >> to use it. >> >> > Start with the manual, where modifications to the topology and relevant > commands and files are described. Then refer to the how-to online, which > has specific instructions. Then, ask specific questions of problems you > are having. I doubt anyone on this list will be able or willing to guess > where your problems are at this point. > > -Justin > > On Thu, Nov 17, 2011 at 10:00 AM, Justin A. Lemkul > jalem...@vt.edu>> wrote: >> >> >> >>Liu, Liang wrote: >> >>Dear all, >> >>I am trying to calculate potentials for RNA structures with a >>serial of tabulated potentials (non-bonded). >>And the only potential I am going to use is the tabulated >>potentials, and the effect from force field should be removed. >>However, when I use pdb2gmx to build the topology file, I have >>to choose a force field. What should I do for that? Thanks. >> >> >>It sounds like you need to be constructing your own force field, >>completely, from scratch. If you're not looking to use the existing >>force fields, this sounds like the only real solution. You can take >>the time to make .xvg files for bonded and nonbonded interactions >>(see the manual), but that is probably just as much work and your >>simulations will be much slower. >> >>-Justin >> >>-- ==**__== >> >> >>Justin A. Lemkul >>Ph.D. Candidate >>ICTAS Doctoral Scholar >>MILES-IGERT Trainee >>Department of Biochemistry >>Virginia Tech >>Blacksburg, VA >>jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080 >> >> >> http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justin<http://vt.edu/Pages/Personal/justin> >> >> <http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> >> > >> >>==**__== >> >>-- gmx-users mailing listgmx-users@gromacs.org >><mailto:gmx-users@gromacs.org> >> >> http://lists.gromacs.org/__**mailman/listinfo/gmx-users<http://lists.gromacs.org/__mailman/listinfo/gmx-users> >> >> >> <http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >> > >>Please search the archive at >> >> http://www.gromacs.org/__**Support/Mailing_Lists/Search<http://www.gromacs.org/__Support/Mailing_Lists/Search> >> >> >> <http://www.gromacs.org/**Support/Mailing_Lists/Search<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 >><mailto:gmx-users-request@**gromacs.org >> >. >>Can't post? Read >> http://www.gromacs.org/__**Support/Mailing_Lists<http://www.gromacs.org/__Support/Mailing_Lists> >> >> >> <http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >> > >> >> >> >> >> -- >> Best, >> Liang Liu >> > > -- > ==**== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==**== > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> > -- Best, Liang Liu -- 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] calculate potential with tabulated non-bonded interactions
Well, I already have the xvg files from others. However I don't know how to use it. On Thu, Nov 17, 2011 at 10:00 AM, Justin A. Lemkul wrote: > > > Liu, Liang wrote: > >> Dear all, >> >> I am trying to calculate potentials for RNA structures with a serial of >> tabulated potentials (non-bonded). >> And the only potential I am going to use is the tabulated potentials, and >> the effect from force field should be removed. >> However, when I use pdb2gmx to build the topology file, I have to choose >> a force field. What should I do for that? Thanks. >> >> > It sounds like you need to be constructing your own force field, > completely, from scratch. If you're not looking to use the existing force > fields, this sounds like the only real solution. You can take the time to > make .xvg files for bonded and nonbonded interactions (see the manual), but > that is probably just as much work and your simulations will be much slower. > > -Justin > > -- > ==**== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==**== > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> > -- Best, Liang Liu -- 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] calculate potential with tabulated non-bonded interactions
Dear all, I am trying to calculate potentials for RNA structures with a serial of tabulated potentials (non-bonded). And the only potential I am going to use is the tabulated potentials, and the effect from force field should be removed. However, when I use pdb2gmx to build the topology file, I have to choose a force field. What should I do for that? Thanks. -- Best, Liang Liu -- 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] calculate potentials of structure
Dear all, I am wondering if there is a way to calculate the potential of a given RNA structure? No minimization, no simulation, but calculate the potential. -- Best, Liang Liu -- 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] about tabulated potentials
Thanks, I will try to figure it out. On Tue, Nov 15, 2011 at 9:50 PM, Mark Abraham wrote: > On 16/11/2011 2:45 PM, Liu, Liang wrote: > > Thanks for help. > If I have more atoms and they can interact each other or itself, like PP, > PC, PN, CP, CN, CC How's the energygrp_table looking like? > I know there should be a option in the grompp, but how to do that? > > > See manual sections 7.3.12 and 6.7.2. > > > And how to generate the index file? I am sorry for so many questions, I > am really not familiar with it. > > > http://www.gromacs.org/Documentation/File_Formats/Index_File > > Mark > > > > On Tue, Nov 15, 2011 at 9:28 PM, Sikandar Mashayak > wrote: > >> >From your system information, I understand that you need to specify >> tabulated potentials between atoms P and P, and between atoms C and P, and >> so on. >> >> To achieve this, you need to create energy groups with atom types P and >> C, and specify energygrp_table options in the grompp such as following >> >> >> >> energygrps = P C ; (and rest of the groups in your system, you will need >> to specify index file containing energy groups ) >> energygrp_table = P P P C >> >> >> >> so now mdrun looks for table_P_P.xvg and table_P_C.xvg in the run >> directory, and uses it for P-P and P-C interactions, whereas for all other >> interactions default table.xvg file is used. >> >> >> I hope this helps. >> >> Regards >> Sikandar >> >> >> On Tue, Nov 15, 2011 at 2:49 PM, Liu, Liang wrote: >> >>> I am trying to use a serial of tabulated potentials, which are the >>> functions of the distance between atoms and the names are table.xvg, >>> table_P_P.xvg, table_C_P.xvg, etc., to do the energy minimization of some >>> RNA structures. >>> The procedure I apply is as following: >>> >>> pdb2gmx -f rna.pdb -o conf.pdb -ff amber03 -water spce >>> editconf -bt octahedron -f conf.pdb -o box.pdb -d 1.0 >>> genbox -cp box.pdb -cs spc216 -o water.pdb -p topol.top >>> grompp -f em.mdp -c water.pdb -p topol.top -o em.tpr -maxwarn 2 >>> mdrun -v -s em.tpr -c em.pdb -table table.xvg >>> >>> And the em.mdp file is: >>> cpp = /usr/bin/cpp; Preprocessor >>> include = -I../top; Directories to include >>> in the topology format >>> define = -DFLEX_SPC >>> integrator = steep ; Algorithm options >>> dt = 0.002; ps ! ; run control, the time >>> step >>> nsteps = 1000; run steps, simulation >>> length = dt*nsteps >>> nstenergy = 10 ; Write energies to disk >>> every nstenergy steps >>> nstxtcout = 10 ; Write coordinates to >>> disk every nstxtcout steps >>> xtc_grps= RNA ; Which coordinate >>> group(s) to write to disk >>> energygrps = RNA ; Whici energy group(s) >>> to write to disk >>> nstlist = 10 ; Frequency to update the >>> neighbor list and long range forces >>> ns_type = grid; Method to determine >>> neighbor list and long range forces (simple, grid) >>> rlist = 1.0 ; Cut-off for making >>> neighbor list (short range forces) >>> vdw-type= user >>> coulombtype = user; Treatment of long range >>> electrostatic interactions >>> rcoulomb= 1.0 ; long range >>> electrostatic cut-off >>> rvdw= 1.0 ; long range Van der >>> Walls cut-off >>> constraints = none >>> pbc = xyz >>> emtol = 5000.0 >>> emstep = 0.01 >>> >>> All the procedure and file are right? Thanks. >>> >>> -- >>> Best, >>> Liang Liu >>> >>> -- >>> 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-use
Re: [gmx-users] about tabulated potentials
Thanks for help. If I have more atoms and they can interact each other or itself, like PP, PC, PN, CP, CN, CC How's the energygrp_table looking like? I know there should be a option in the grompp, but how to do that? And how to generate the index file? I am sorry for so many questions, I am really not familiar with it. On Tue, Nov 15, 2011 at 9:28 PM, Sikandar Mashayak wrote: > >From your system information, I understand that you need to specify > tabulated potentials between atoms P and P, and between atoms C and P, and > so on. > > To achieve this, you need to create energy groups with atom types P and C, > and specify energygrp_table options in the grompp such as following > > > > energygrps = P C ; (and rest of the groups in your system, you will need > to specify index file containing energy groups ) > energygrp_table = P P P C > > > > so now mdrun looks for table_P_P.xvg and table_P_C.xvg in the run > directory, and uses it for P-P and P-C interactions, whereas for all other > interactions default table.xvg file is used. > > > I hope this helps. > > Regards > Sikandar > > > On Tue, Nov 15, 2011 at 2:49 PM, Liu, Liang wrote: > >> I am trying to use a serial of tabulated potentials, which are the >> functions of the distance between atoms and the names are table.xvg, >> table_P_P.xvg, table_C_P.xvg, etc., to do the energy minimization of some >> RNA structures. >> The procedure I apply is as following: >> >> pdb2gmx -f rna.pdb -o conf.pdb -ff amber03 -water spce >> editconf -bt octahedron -f conf.pdb -o box.pdb -d 1.0 >> genbox -cp box.pdb -cs spc216 -o water.pdb -p topol.top >> grompp -f em.mdp -c water.pdb -p topol.top -o em.tpr -maxwarn 2 >> mdrun -v -s em.tpr -c em.pdb -table table.xvg >> >> And the em.mdp file is: >> cpp = /usr/bin/cpp; Preprocessor >> include = -I../top; Directories to include >> in the topology format >> define = -DFLEX_SPC >> integrator = steep ; Algorithm options >> dt = 0.002; ps ! ; run control, the time >> step >> nsteps = 1000; run steps, simulation >> length = dt*nsteps >> nstenergy = 10 ; Write energies to disk >> every nstenergy steps >> nstxtcout = 10 ; Write coordinates to >> disk every nstxtcout steps >> xtc_grps= RNA ; Which coordinate >> group(s) to write to disk >> energygrps = RNA ; Whici energy group(s) to >> write to disk >> nstlist = 10 ; Frequency to update the >> neighbor list and long range forces >> ns_type = grid; Method to determine >> neighbor list and long range forces (simple, grid) >> rlist = 1.0 ; Cut-off for making >> neighbor list (short range forces) >> vdw-type= user >> coulombtype = user; Treatment of long range >> electrostatic interactions >> rcoulomb= 1.0 ; long range electrostatic >> cut-off >> rvdw= 1.0 ; long range Van der Walls >> cut-off >> constraints = none >> pbc = xyz >> emtol = 5000.0 >> emstep = 0.01 >> >> All the procedure and file are right? Thanks. >> >> -- >> Best, >> Liang Liu >> >> -- >> 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 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 > -- Best, Liang Liu -- 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] about tabulated potentials
I am trying to use a serial of tabulated potentials, which are the functions of the distance between atoms and the names are table.xvg, table_P_P.xvg, table_C_P.xvg, etc., to do the energy minimization of some RNA structures. The procedure I apply is as following: pdb2gmx -f rna.pdb -o conf.pdb -ff amber03 -water spce editconf -bt octahedron -f conf.pdb -o box.pdb -d 1.0 genbox -cp box.pdb -cs spc216 -o water.pdb -p topol.top grompp -f em.mdp -c water.pdb -p topol.top -o em.tpr -maxwarn 2 mdrun -v -s em.tpr -c em.pdb -table table.xvg And the em.mdp file is: cpp = /usr/bin/cpp; Preprocessor include = -I../top; Directories to include in the topology format define = -DFLEX_SPC integrator = steep ; Algorithm options dt = 0.002; ps ! ; run control, the time step nsteps = 1000; run steps, simulation length = dt*nsteps nstenergy = 10 ; Write energies to disk every nstenergy steps nstxtcout = 10 ; Write coordinates to disk every nstxtcout steps xtc_grps= RNA ; Which coordinate group(s) to write to disk energygrps = RNA ; Whici energy group(s) to write to disk nstlist = 10 ; Frequency to update the neighbor list and long range forces ns_type = grid; Method to determine neighbor list and long range forces (simple, grid) rlist = 1.0 ; Cut-off for making neighbor list (short range forces) vdw-type= user coulombtype = user; Treatment of long range electrostatic interactions rcoulomb= 1.0 ; long range electrostatic cut-off rvdw= 1.0 ; long range Van der Walls cut-off constraints = none pbc = xyz emtol = 5000.0 emstep = 0.01 All the procedure and file are right? Thanks. -- Best, Liang Liu -- 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] import force field
The tabulated potentials I am using is non-bonded interactions. The question is the application of these potentials will only modify the force field, e.g. amber03, or will take place of the force field? On Mon, Nov 14, 2011 at 6:40 PM, Mark Abraham wrote: > On 15/11/2011 9:33 AM, Liu, Liang wrote: > > I have a serial of tabulated potentials with the name of *.xvg, which are > the function of atom distance. > I am wondering how to use them in gromacs simulation? Will that replace > the force field, e.g. amber03? Thanks. > > > There are sections in the manual that describe the use of tabulated > potentials for either bonded or non-bonded interactions. Such tables modify > the force field in the expected manner. > > 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 > -- Best, Liang Liu -- 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] how to select option for genion command automatically?
Yes, I found it. THanks. On Mon, Nov 14, 2011 at 9:45 PM, Terry wrote: > > This is what you are looking for: > > > http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts?highlight=scripting > > Terry > > > On Tue, Nov 15, 2011 at 11:42 AM, Liu, Liang wrote: > >> I am wondering if there is a flag to make the command select SOL >> automatically instead of pressing some number each time? I have thousands >> of structures, it is really time-consuming to select one by one. >> >> -- >> Best, >> Liang Liu >> >> -- >> 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 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 > -- Best, Liang Liu -- 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] how to select option for genion command automatically?
I am wondering if there is a flag to make the command select SOL automatically instead of pressing some number each time? I have thousands of structures, it is really time-consuming to select one by one. -- Best, Liang Liu -- 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] import force field
I have a serial of tabulated potentials with the name of *.xvg, which are the function of atom distance. I am wondering how to use them in gromacs simulation? Will that replace the force field, e.g. amber03? Thanks. -- Best, Liang Liu -- 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] GMX to remove clashes?
Thanks. Do you know how to use a new force field, not amber or charm, but a force field built by someone else, and it's already in Gromacs format (tons of xvg file, right?) On Mon, Nov 14, 2011 at 4:13 PM, Justin A. Lemkul wrote: > > > Liu, Liang wrote: > >> This is a "reasonable" answer :) >> >> Thanks for that, and I just tried Gromacs for minimization, and looks the >> final structure does not have clashes anymore, and also are very close to >> the initial structure. >> >> Another question is if there is a way to add ions automatically, meaning >> no need to check the "NOTE" of "System has non-zero total charge" in the >> output of grompp command? And also update the topology file automatically >> too? >> >> > That depends on the system. For a simple solute in water, the running > total charge of the solute is recorded in the qtot column of the .top file. > If you have a complex system with lots of charged things, no, there is no > convenient way to get the charge aside from calculating it by hand or > reading the grompp output. > > The topology can be modified automatically by genion after ions are added > by using the -p flag. > > -Justin > > On Mon, Nov 14, 2011 at 3:49 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote: >> >> >> >>Liu, Liang wrote: >> >>Hi, all, >>I am wondering if Gromacs can do the following work? >> >>Assuming I have a pdb file of an RNA molecule. Some atoms may be >>too close or even overlap, I am wondering if Gromacs can move >>the atoms to reasonable positions and remove the bad contacts? >>The final structure is supposed to be the "most" stable >>structure with minimal energy. I know AMBER minimization can do >>this work, and I am wondering if Gromacs can do the same? >> >> >>Gromacs is perfectly capable of energy minimization. Whether or not >>minimization succeeds and gives a reasonable output is mostly >>dependent upon the feasibility of the starting structure. If the >>minimization crashes, it's not Gromacs' fault ;) >> >>-Justin >> >>-- ==**__== >> >> >>Justin A. Lemkul >>Ph.D. Candidate >>ICTAS Doctoral Scholar >>MILES-IGERT Trainee >>Department of Biochemistry >>Virginia Tech >>Blacksburg, VA >>jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080 >> >> >> http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justin<http://vt.edu/Pages/Personal/justin> >> >> <http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> >> > >> >>==**__== >> >>-- gmx-users mailing listgmx-users@gromacs.org >><mailto:gmx-users@gromacs.org> >> >> http://lists.gromacs.org/__**mailman/listinfo/gmx-users<http://lists.gromacs.org/__mailman/listinfo/gmx-users> >> >> >> <http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >> > >>Please search the archive at >> >> http://www.gromacs.org/__**Support/Mailing_Lists/Search<http://www.gromacs.org/__Support/Mailing_Lists/Search> >> >> >> <http://www.gromacs.org/**Support/Mailing_Lists/Search<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 >><mailto:gmx-users-request@**gromacs.org >> >. >>Can't post? Read >> http://www.gromacs.org/__**Support/Mailing_Lists<http://www.gromacs.org/__Support/Mailing_Lists> >> >> >> <http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >> > >> >> >> >> >> -- >> Best, >> Liang Liu >> > > -- > ==**== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==**
Re: [gmx-users] GMX to remove clashes?
This is a "reasonable" answer :) Thanks for that, and I just tried Gromacs for minimization, and looks the final structure does not have clashes anymore, and also are very close to the initial structure. Another question is if there is a way to add ions automatically, meaning no need to check the "NOTE" of "System has non-zero total charge" in the output of grompp command? And also update the topology file automatically too? On Mon, Nov 14, 2011 at 3:49 PM, Justin A. Lemkul wrote: > > > Liu, Liang wrote: > >> Hi, all, >> I am wondering if Gromacs can do the following work? >> >> Assuming I have a pdb file of an RNA molecule. Some atoms may be too >> close or even overlap, I am wondering if Gromacs can move the atoms to >> reasonable positions and remove the bad contacts? The final structure is >> supposed to be the "most" stable structure with minimal energy. I know >> AMBER minimization can do this work, and I am wondering if Gromacs can do >> the same? >> >> > Gromacs is perfectly capable of energy minimization. Whether or not > minimization succeeds and gives a reasonable output is mostly dependent > upon the feasibility of the starting structure. If the minimization > crashes, it's not Gromacs' fault ;) > > -Justin > > -- > ==**== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==**== > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> > -- Best, Liang Liu -- 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] GMX to remove clashes?
Hi, all, I am wondering if Gromacs can do the following work? Assuming I have a pdb file of an RNA molecule. Some atoms may be too close or even overlap, I am wondering if Gromacs can move the atoms to reasonable positions and remove the bad contacts? The final structure is supposed to be the "most" stable structure with minimal energy. I know AMBER minimization can do this work, and I am wondering if Gromacs can do the same? -- Best, Liang Liu -- 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] How to obtain structures with large RMSD?
Well, the thing is even I turn off the position restraint and raise the temperature to 600k, the RMSD I can obtained is only about 0.3 for a RNA hairpin. -- 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] How to obtain structures with large RMSD?
Well, I am only trying to get structures with some of them far from the initial structure (large RMSD) and some of them close to the initial one... On Mon, Oct 10, 2011 at 10:37 AM, Tsjerk Wassenaar wrote: > Hi Liang Liu, > > You will never get broader sampling by adding restraints. If you want > to have broader sampling, raise the temperature or add denaturants. > But also ask yourself the question if what you think you want is what > you should be wanting. What is the actual question you're trying to > solve? > > Cheers, > > Tsjerk > > On Mon, Oct 10, 2011 at 5:32 PM, Liu, Liang wrote: > > How's position restraint? If the force constant is reduced (reduce the > > number in posre.itp ?), the simulation will lead to more flexible > structure? > > > > On Mon, Oct 10, 2011 at 10:20 AM, Justin A. Lemkul > wrote: > >> > >> > >> Liu, Liang wrote: > >>> > >>> Thanks. > >>> > >>> Will the constrain help? > >>> > >> > >> Bond constraints? Well, in general, they're useful, and likely > necessary > >> at high temperature to keep your system stable. Please be more > specific. > >> > >> -Justin > >> > >>> On Mon, Oct 10, 2011 at 10:06 AM, Justin A. Lemkul >>> <mailto:jalem...@vt.edu>> wrote: > >>> > >>> > >>> > >>>Liu, Liang wrote: > >>> > >>>Hi, all, > >>> > >>>I am trying to use Gromacs to obtain structural ensembles around > >>>native structures (PDB structures). > >>>However the simulated structures are always very close to the > >>>initial one, with RMSD < 0.2. > >>>I am wondering how to obtain large-RMSD structures? Thanks. > >>> > >>> > >>>Large RMSD values would indicate non-native structures, which > >>>doesn't sound like what you're looking for. If your goal is simply > >>>enhanced sampling, try REMD. > >>> > >>>-Justin > >>> > >>>-- ==__== > >>> > >>>Justin A. Lemkul > >>>Ph.D. Candidate > >>>ICTAS Doctoral Scholar > >>>MILES-IGERT Trainee > >>>Department of Biochemistry > >>>Virginia Tech > >>>Blacksburg, VA > >>>jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080 > >>> > >>>http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin > >>><http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > >>> > >>>==__== > >>>-- gmx-users mailing listgmx-users@gromacs.org > >>><mailto:gmx-users@gromacs.org> > >>>http://lists.gromacs.org/__mailman/listinfo/gmx-users > >>><http://lists.gromacs.org/mailman/listinfo/gmx-users> > >>>Please search the archive at > >>>http://www.gromacs.org/__Support/Mailing_Lists/Search > >>><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 > >>><mailto:gmx-users-requ...@gromacs.org>. > >>>Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists > >>><http://www.gromacs.org/Support/Mailing_Lists> > >>> > >>> > >>> > >>> > >>> -- > >>> Best, > >>> Liang Liu > >> > >> -- > >> > >> > >> Justin A. Lemkul > >> Ph.D. Candidate > >> ICTAS Doctoral Scholar > >> MILES-IGERT Trainee > >> 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 t
Re: [gmx-users] How to obtain structures with large RMSD?
How's position restraint? If the force constant is reduced (reduce the number in posre.itp ?), the simulation will lead to more flexible structure? On Mon, Oct 10, 2011 at 10:20 AM, Justin A. Lemkul wrote: > > > Liu, Liang wrote: > >> Thanks. >> >> Will the constrain help? >> >> > Bond constraints? Well, in general, they're useful, and likely necessary > at high temperature to keep your system stable. Please be more specific. > > -Justin > > On Mon, Oct 10, 2011 at 10:06 AM, Justin A. Lemkul > jalem...@vt.edu>> wrote: >> >> >> >>Liu, Liang wrote: >> >>Hi, all, >> >>I am trying to use Gromacs to obtain structural ensembles around >>native structures (PDB structures). >>However the simulated structures are always very close to the >>initial one, with RMSD < 0.2. >>I am wondering how to obtain large-RMSD structures? Thanks. >> >> >>Large RMSD values would indicate non-native structures, which >>doesn't sound like what you're looking for. If your goal is simply >>enhanced sampling, try REMD. >> >>-Justin >> >>-- ==**__== >> >> >>Justin A. Lemkul >>Ph.D. Candidate >>ICTAS Doctoral Scholar >>MILES-IGERT Trainee >>Department of Biochemistry >>Virginia Tech >>Blacksburg, VA >>jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080 >> >> >> http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justin<http://vt.edu/Pages/Personal/justin> >> >> <http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> >> > >> >>==**__== >> >>-- gmx-users mailing listgmx-users@gromacs.org >><mailto:gmx-users@gromacs.org> >> >> http://lists.gromacs.org/__**mailman/listinfo/gmx-users<http://lists.gromacs.org/__mailman/listinfo/gmx-users> >> >> >> <http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >> > >>Please search the archive at >> >> http://www.gromacs.org/__**Support/Mailing_Lists/Search<http://www.gromacs.org/__Support/Mailing_Lists/Search> >> >> >> <http://www.gromacs.org/**Support/Mailing_Lists/Search<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 >><mailto:gmx-users-request@**gromacs.org >> >. >>Can't post? Read >> http://www.gromacs.org/__**Support/Mailing_Lists<http://www.gromacs.org/__Support/Mailing_Lists> >> >> >> <http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >> > >> >> >> >> >> -- >> Best, >> Liang Liu >> > > -- > ==**== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==**== > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> > -- Best, Liang Liu -- 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] How to obtain structures with large RMSD?
Thanks. Will the constrain help? On Mon, Oct 10, 2011 at 10:06 AM, Justin A. Lemkul wrote: > > > Liu, Liang wrote: > >> Hi, all, >> >> I am trying to use Gromacs to obtain structural ensembles around native >> structures (PDB structures). >> However the simulated structures are always very close to the initial one, >> with RMSD < 0.2. >> I am wondering how to obtain large-RMSD structures? Thanks. >> >> > Large RMSD values would indicate non-native structures, which doesn't sound > like what you're looking for. If your goal is simply enhanced sampling, try > REMD. > > -Justin > > -- > ==**== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==**== > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> > -- Best, Liang Liu -- 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] How to obtain structures with large RMSD?
Hi, all, I am trying to use Gromacs to obtain structural ensembles around native structures (PDB structures). However the simulated structures are always very close to the initial one, with RMSD < 0.2. I am wondering how to obtain large-RMSD structures? Thanks. -- Best, Liang Liu -- 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] REMD problem
Thanks. Actually I applied just because the tutorial said so :( What I need is the structures only, I googled, but did not obtain useful information about Gromacs with REMD. Maybe I need to read the manual again :( I am totally fresh to MD simulation, just worked on this for 1 week ... On Thu, Sep 29, 2011 at 4:24 PM, Mark Abraham wrote: > On 30/09/2011 2:50 AM, Liu, Liang wrote: > > After running for more than 12 hours, the REMD simulation is completed and > what I get is 50 log, 50 trr, 50 cpt and 50 tpr files. > > > Yep. One for each simulation. > > > Not sure if the result is reasonable. > > > Justin told you yesterday they would not be, because you have made a number > of totally arbitrary choices. > > > I tried to analyze the result, and after applying demux.pl, two > files replica_index.xvg replica_temp.xvg are obtained. > > > Why did you want to demux? > > > My question is how to obtain the structure information? (I will need pdb > file). > > > Do all the tutorial material you can find - even if not strictly relevant - > to get an idea about good workflows. Then try to replicate (part of) a > published REMD study to see how things work there. Search the web and check > out the GROMACS web page - there's lots of material out there. Stabbing in > the dark is a great way to waste your time, and people here don't have the > time to teach every person every thing. > > 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 > -- Best, Liang Liu -- 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] REMD problem
After running for more than 12 hours, the REMD simulation is completed and what I get is 50 log, 50 trr, 50 cpt and 50 tpr files. Not sure if the result is reasonable. I tried to analyze the result, and after applying demux.pl, two files replica_index.xvg replica_temp.xvg are obtained. My question is how to obtain the structure information? (I will need pdb file). -- 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] REMD problem
After running for more than 12 hours, the REMD simulation is completed and what I get is 50 log, 50 trr, 50 cpt and 50 tpr files. Not sure if the result is reasonable. I tried to analyze the result, and after applying demux.pl, two files replica_index.xvg replica_temp.xvg are obtained. My question is how to obtain the structure information? (I will need pdb file). On Thu, Sep 29, 2011 at 6:23 AM, Manuel Prinz wrote: > Am Do, 29.09.2011, 01:38 schrieb Mark Abraham: > > If the MPI configuration allows physical processors to be > > over-allocated, then GROMACS is none the wiser. > > Over-allocation is the default in Open MPI[1]. So it's technically > possible to run 50 MPI processes on 2 cores. Whether or not this is a good > idea is left on as an exercise to the reader. ;) > > Best regards, > Manuel > > [1] When not run from a resource manager that takes care of setting the > "right" configuration options. > > -- > 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 > -- Best, Liang Liu -- 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] REMD problem
Not know. I will update the result tomorrow, as the 5 steps take really long time :( On Wed, Sep 28, 2011 at 4:38 PM, Mark Abraham wrote: > On 29/09/2011 7:20 AM, Justin A. Lemkul wrote: > >> >> >> Liu, Liang wrote: >> >>> Yes, they are updated like: >>> ... >>> Replica exchange at step 5700 time 11.4 >>> Repl ex 01 x 23 x 45 x 6789 x 10 11 x 12 >>> 13 14 15 x 16 17 x 18 19 x 20 21 x 22 23 24 25 x 26 27 >>> 28 29 x 30 31 32 33 x 34 35 36 37 x 38 39 40 41 x 42 >>> 43 x 44 45 x 46 47 48 49 >>> Repl pr1.0 1.0 1.0 .00 1.0 1.0 >>> .00 1.0 1.0 1.0 1.0 .00 1.0 .00 >>> 1.0 .00 1.0 .00 .46 .00 1.0 >>> .78 1.0 .00 >>> >>> Replica exchange at step 5750 time 11.5 >>> Repl 0 <-> 1 dE = -7.583e+00 >>> Repl ex 0 x 1234 x 56 x 78 x 9 10 x 11 12 x >>> 13 14 x 15 16 x 17 18 x 19 20 21 22 23 24 x 25 26 27 >>> 28 x 29 30 31 32 x 33 34 35 36 37 38 39 40 x 41 42 x >>> 43 44 45 46 47 48 49 >>> Repl pr 1.0 .00 1.0 1.0 1.0 1.0 1.0 >>> 1.0 1.0 1.0 .48 .11 1.0 .00 >>> 1.0 .00 1.0 .00 .00 .01 1.0 1.0 >>> .00 .01 .01 >>> >>> Step Time Lambda >>> 5800 11.60.0 >>> >>> Energies (kJ/mol) >>> AngleProper Dih. Improper Dih. LJ-14 >>> Coulomb-14 >>>9.69806e+021.32207e+033.34938e+014.93171e+02 >>> -3.9e+03 >>>LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Position >>> Rest. >>>3.14374e+04 -6.42258e+02 -1.88529e+05 -2.01604e+04 >>> 0.0e+00 >>> PotentialKinetic En. Total Energy Conserved En. >>> Temperature >>> -1.78987e+054.57462e+04 -1.33240e+051.23302e+10 >>> 5.62201e+02 >>> Pres. DC (bar) Pressure (bar) Constr. rmsd >>> -2.12803e+02 -5.47109e+022.21484e-05 >>> ... >>> >>> >> Perhaps someone else can offer an explanation. It should not be possible >> to run multiple replicas on a single processor. Also note that your >> exchange probability is extremely high; you're likely not obtaining >> meaningful sampling. >> > > If the MPI configuration allows physical processors to be over-allocated, > then GROMACS is none the wiser. > > Mark > > > >> -Justin >> >> On Wed, Sep 28, 2011 at 4:08 PM, Justin A. Lemkul >> jalem...@vt.edu>> wrote: >>> >>> >>> >>>Liu, Liang wrote: >>> >>>Thanks. currently what I see is the program runs very slowly, >>>but get .log file for all the 50 replicas, does this mean all of >>>them are running? >>> >>> >>>Are the log files being updated, or do they all simply contain a >>>fatal error message that there are insufficient nodes? I cannot >>>think of a reason why 50 simulations could possibly run on 2 >>> processors. >>> >>>-Justin >>> >>>On Wed, Sep 28, 2011 at 3:41 PM, Justin A. Lemkul >>> mailto:jalem...@vt.edu> >>> <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> wrote: >>> >>> >>> >>> Liu, Liang wrote: >>> >>> Well, although this makes sense, why all the 50 replicas >>> are >>> running when I run "mpirun >>> -np 50 mdrun_mpi -s md.tpr -multi 50 -replex 50" on >>>my own >>> computer with only 2 cores? >>> >>> >>> I can offer no explanation for this behavior, but I expect that >>> either not all of them are actually running, or at the very >>> least >>> you will get horribly slow performance. >>> >>> >>> By the way, would you please show me where I can find the >>> reasonable replex number information in the literature? >>> I did >>> not find it in the link you posted and th
Re: [gmx-users] REMD problem
Yes, they are updated like: ... Replica exchange at step 5700 time 11.4 Repl ex 01 x 23 x 45 x 6789 x 10 11 x 12 13 14 15 x 16 17 x 18 19 x 20 21 x 22 23 24 25 x 26 27 28 29 x 30 31 32 33 x 34 35 36 37 x 38 39 40 41 x 42 43 x 44 45 x 46 47 48 49 Repl pr1.0 1.0 1.0 .00 1.0 1.0 .00 1.0 1.0 1.0 1.0 .00 1.0 .00 1.0 .00 1.0 .00 .46 .00 1.0 .78 1.0 .00 Replica exchange at step 5750 time 11.5 Repl 0 <-> 1 dE = -7.583e+00 Repl ex 0 x 1234 x 56 x 78 x 9 10 x 11 12 x 13 14 x 15 16 x 17 18 x 19 20 21 22 23 24 x 25 26 27 28 x 29 30 31 32 x 33 34 35 36 37 38 39 40 x 41 42 x 43 44 45 46 47 48 49 Repl pr 1.0 .00 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 .48 .11 1.0 .00 1.0 .00 1.0 .00 .00 .01 1.0 1.0 .00 .01 .01 Step Time Lambda 5800 11.60.0 Energies (kJ/mol) AngleProper Dih. Improper Dih. LJ-14 Coulomb-14 9.69806e+021.32207e+033.34938e+014.93171e+02 -3.9e+03 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Position Rest. 3.14374e+04 -6.42258e+02 -1.88529e+05 -2.01604e+040.0e+00 PotentialKinetic En. Total Energy Conserved En.Temperature -1.78987e+054.57462e+04 -1.33240e+051.23302e+105.62201e+02 Pres. DC (bar) Pressure (bar) Constr. rmsd -2.12803e+02 -5.47109e+022.21484e-05 ... On Wed, Sep 28, 2011 at 4:08 PM, Justin A. Lemkul wrote: > > > Liu, Liang wrote: > >> Thanks. currently what I see is the program runs very slowly, but get .log >> file for all the 50 replicas, does this mean all of them are running? >> >> > Are the log files being updated, or do they all simply contain a fatal > error message that there are insufficient nodes? I cannot think of a reason > why 50 simulations could possibly run on 2 processors. > > -Justin > > On Wed, Sep 28, 2011 at 3:41 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote: >> >> >> >>Liu, Liang wrote: >> >>Well, although this makes sense, why all the 50 replicas are >>running when I run "mpirun >> -np 50 mdrun_mpi -s md.tpr -multi 50 -replex 50" on my own >>computer with only 2 cores? >> >> >>I can offer no explanation for this behavior, but I expect that >>either not all of them are actually running, or at the very least >>you will get horribly slow performance. >> >> >>By the way, would you please show me where I can find the >>reasonable replex number information in the literature? I did >>not find it in the link you posted and the manual either. >> >> >>A few minutes of real literature searching will be far more valuable >>than some random person on the Internet giving you a value that you >>blindly use ;) >> >>-Justin >> >>Thanks. >> >> >>-- Best, >>Liang Liu >> >> >>-- ==**__== >> >>Justin A. Lemkul >>Ph.D. Candidate >>ICTAS Doctoral Scholar >>MILES-IGERT Trainee >>Department of Biochemistry >>Virginia Tech >>Blacksburg, VA >>jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080 >> >> >> >> http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justin<http://vt.edu/Pages/Personal/justin> >> >> <http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> >> > >> >>==**__== >>-- gmx-users mailing listgmx-users@gromacs.org >><mailto:gmx-users@gromacs.org> >> >> >> http://lists.gromacs.org/__**mailman/listinfo/gmx-users<http://lists.gromacs.org/__mailman/listinfo/gmx-users> >> >> <http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >> > >>Please search the archive at >> >> http://www.gromacs.org/__**Support/Mailing_Lists/Search<http://www.gromacs.org/__Support/Mailing_Lists/Search> >> >> <http://www.gromacs.org/**Support/Mailing_Lists/Sear
Re: [gmx-users] REMD problem
Thanks. currently what I see is the program runs very slowly, but get .log file for all the 50 replicas, does this mean all of them are running? On Wed, Sep 28, 2011 at 3:41 PM, Justin A. Lemkul wrote: > > > Liu, Liang wrote: > >> Well, although this makes sense, why all the 50 replicas are running when >> I run "mpirun >> -np 50 mdrun_mpi -s md.tpr -multi 50 -replex 50" on my own computer >> with only 2 cores? >> >> > I can offer no explanation for this behavior, but I expect that either not > all of them are actually running, or at the very least you will get horribly > slow performance. > > > By the way, would you please show me where I can find the reasonable >> replex number information in the literature? I did not find it in the link >> you posted and the manual either. >> >> > A few minutes of real literature searching will be far more valuable than > some random person on the Internet giving you a value that you blindly use > ;) > > -Justin > > Thanks. >> >> >> -- >> Best, >> Liang Liu >> > > -- > ==**== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==**== > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> > -- Best, Liang Liu -- 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] REMD problem
Well, although this makes sense, why all the 50 replicas are running when I run "mpirun -np 50 mdrun_mpi -s md.tpr -multi 50 -replex 50" on my own computer with only 2 cores? By the way, would you please show me where I can find the reasonable replex number information in the literature? I did not find it in the link you posted and the manual either. Thanks. -- Best, Liang Liu -- 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] REMD problem
So if my personal computer have 2 cores, the np should be set to 2? Does it relate to -multi? How to choose a reasonable number for -replex? the smaller the better? Thanks again. On Wed, Sep 28, 2011 at 3:06 PM, Justin A. Lemkul wrote: > > > Liu, Liang wrote: > >> This works. Thanks a lot. >> >> Currently I am running on an RNA molecule and I want to a 1 ns REMD >> simulations with 50 temperatures, >> would you please have a look at the following command "mpirun -np 50 >> mdrun_mpi -s md.tpr -multi 50 -replex 50". Is this right? >> How to choose the numbers for np, multi or replex? >> >> > Current Gromacs versions allow more than one processor per REMD simulation. > Please refer to the link I provided before for specifics. You need all of > the replicas to run at roughly the same speed so the number of processors > per simulation should be the same. > > > Is the simulation time still set in the mdp file with nsteps and dt? e.g. >> nsteps = 50 and dt = 0.002 to run a 1ns simulation? >> >> > It's just like any other simulation in this regard. > > -Justin > > Any helps will be highly appreciated. >> >> On Wed, Sep 28, 2011 at 1:27 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote: >> >> >> >>Liu, Liang wrote: >> >>Thanks for the information. I installed the mpi version with >>"sudo apt-get install gromacs-openmpi" under Ubuntu. >> >>Then run "mdrun_mpi -s md.tpr -replex 10 -multi 10"? Another >>error appears, "The number of nodes (1) is not a multiple of the >>number of simulations (10)". What is this for? >> >> >>You have to run mdrun_mpi as a process under mpirun, e.g.: >> >>mpirun -np 10 mdrun_mpi -s md.tpr (etc) >> >>-Justin >> >>On Wed, Sep 28, 2011 at 1:02 PM, Justin A. Lemkul >>mailto:jalem...@vt.edu> >><mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> wrote: >> >> >> >> Liu, Liang wrote: >> >> Does that mean I have to use MPI? I got an error "mdrun >>-multi >> is not supported with the thread library.Please compile >>GROMACS >> with MPI support" after run "mdrun -s md.tpr -multi 10 >>-replex 10" >> >> >> Per the error message, yes. >> >> -Justin >> >> On Wed, Sep 28, 2011 at 12:58 PM, Justin A. Lemkul >> mailto:jalem...@vt.edu> >><mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>> >> <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu> >><mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>>> wrote: >> >> >> >> Liu, Liang wrote: >> >> Hi everyone, >> I tried to use Gromacs to run REMD simulation. >> Firstly a set of (md#).mdp file are make and the >>grompp >> command >> can generate the same amount of (md#).tpr file. >> Assume # = 10, >> then I tried to run REMD as mdrun -s md.tpr -np 10 >> -replex 10. >> >> However, a fetal error shows as "Need at least two >> replicas for >> replica exchange (option -multi)", what is this >>for? Thanks. >> >> >> >> You have to use the -multi flag. Otherwise all mdrun >>does is run >> md.tpr and try to do REMD with nothing. >> >>http://www.gromacs.org/__** >> Documentation/How-tos/REMD#___**___Execution_Steps<http://www.gromacs.org/__Documentation/How-tos/REMD#__Execution_Steps> >><http://www.gromacs.org/**Documentation/How-tos/REMD#___** >> _Execution_Steps<http://www.gromacs.org/Documentation/How-tos/REMD#Execution_Steps> >> > >> <http://www.gromacs.org/** >> Documentation/How-tos/REMD#___**_Execution_Steps<http://www.gromacs.org/Documentation/How-tos/REMD#Execution_Steps> >><http://www.gromacs.org/__**Documentation/How-tos/REMD#__** >> Execution_Steps<http://www.gromacs.org/__Documentation/How-tos/REMD#__Execution_Steps> >> >> >>
Re: [gmx-users] REMD problem
This works. Thanks a lot. Currently I am running on an RNA molecule and I want to a 1 ns REMD simulations with 50 temperatures, would you please have a look at the following command "mpirun -np 50 mdrun_mpi -s md.tpr -multi 50 -replex 50". Is this right? How to choose the numbers for np, multi or replex? Is the simulation time still set in the mdp file with nsteps and dt? e.g. nsteps = 50 and dt = 0.002 to run a 1ns simulation? Any helps will be highly appreciated. On Wed, Sep 28, 2011 at 1:27 PM, Justin A. Lemkul wrote: > > > Liu, Liang wrote: > >> Thanks for the information. I installed the mpi version with "sudo apt-get >> install gromacs-openmpi" under Ubuntu. >> >> Then run "mdrun_mpi -s md.tpr -replex 10 -multi 10"? Another error >> appears, "The number of nodes (1) is not a multiple of the number of >> simulations (10)". What is this for? >> >> > You have to run mdrun_mpi as a process under mpirun, e.g.: > > mpirun -np 10 mdrun_mpi -s md.tpr (etc) > > -Justin > > On Wed, Sep 28, 2011 at 1:02 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote: >> >> >> >>Liu, Liang wrote: >> >>Does that mean I have to use MPI? I got an error "mdrun -multi >>is not supported with the thread library.Please compile GROMACS >>with MPI support" after run "mdrun -s md.tpr -multi 10 -replex 10" >> >> >>Per the error message, yes. >> >>-Justin >> >>On Wed, Sep 28, 2011 at 12:58 PM, Justin A. Lemkul >>mailto:jalem...@vt.edu> >><mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> wrote: >> >> >> >> Liu, Liang wrote: >> >> Hi everyone, >> I tried to use Gromacs to run REMD simulation. >> Firstly a set of (md#).mdp file are make and the grompp >>command >> can generate the same amount of (md#).tpr file. >> Assume # = 10, >> then I tried to run REMD as mdrun -s md.tpr -np 10 >>-replex 10. >> >> However, a fetal error shows as "Need at least two >>replicas for >> replica exchange (option -multi)", what is this for? Thanks. >> >> >> >> You have to use the -multi flag. Otherwise all mdrun does is >> run >> md.tpr and try to do REMD with nothing. >> >> http://www.gromacs.org/** >> Documentation/How-tos/REMD#___**_Execution_Steps<http://www.gromacs.org/Documentation/How-tos/REMD#Execution_Steps> >><http://www.gromacs.org/__**Documentation/How-tos/REMD#__** >> Execution_Steps<http://www.gromacs.org/__Documentation/How-tos/REMD#__Execution_Steps> >> > >> <http://www.gromacs.org/__** >> Documentation/How-tos/REMD#__**Execution_Steps<http://www.gromacs.org/__Documentation/How-tos/REMD#__Execution_Steps> >><http://www.gromacs.org/**Documentation/How-tos/REMD#** >> Execution_Steps<http://www.gromacs.org/Documentation/How-tos/REMD#Execution_Steps> >> >> >> >> -Justin >> >> -- ==**== >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> MILES-IGERT Trainee >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540) >> >>231-9080 >> >> >> http://www.bevanlab.biochem.__**__vt.edu/Pages/Personal/justin >> >> <http://vt.edu/Pages/Personal/**justin<http://vt.edu/Pages/Personal/justin> >> > >> >> <http://www.bevanlab.biochem._**_vt.edu/Pages/Personal/justin >> >> <http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> >> >> >> >> ==**== >> -- gmx-users mailing listgmx-users@gromacs.org >><mailto:gmx-users@gromacs.org> >> <mailto:gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>**> >> >> >> >> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >> &
Re: [gmx-users] REMD problem
Thanks for the information. I installed the mpi version with "sudo apt-get install gromacs-openmpi" under Ubuntu. Then run "mdrun_mpi -s md.tpr -replex 10 -multi 10"? Another error appears, "The number of nodes (1) is not a multiple of the number of simulations (10)". What is this for? On Wed, Sep 28, 2011 at 1:02 PM, Justin A. Lemkul wrote: > > > Liu, Liang wrote: > >> Does that mean I have to use MPI? I got an error "mdrun -multi is not >> supported with the thread library.Please compile GROMACS with MPI support" >> after run "mdrun -s md.tpr -multi 10 -replex 10" >> >> > Per the error message, yes. > > -Justin > > On Wed, Sep 28, 2011 at 12:58 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote: >> >> >> >>Liu, Liang wrote: >> >>Hi everyone, >>I tried to use Gromacs to run REMD simulation. >>Firstly a set of (md#).mdp file are make and the grompp command >>can generate the same amount of (md#).tpr file. >>Assume # = 10, >>then I tried to run REMD as mdrun -s md.tpr -np 10 -replex 10. >> >>However, a fetal error shows as "Need at least two replicas for >>replica exchange (option -multi)", what is this for? Thanks. >> >> >> >>You have to use the -multi flag. Otherwise all mdrun does is run >>md.tpr and try to do REMD with nothing. >> >>http://www.gromacs.org/__**Documentation/How-tos/REMD#__** >> Execution_Steps<http://www.gromacs.org/__Documentation/How-tos/REMD#__Execution_Steps> >> >> <http://www.gromacs.org/**Documentation/How-tos/REMD#**Execution_Steps<http://www.gromacs.org/Documentation/How-tos/REMD#Execution_Steps> >> > >> >>-Justin >> >>-- ==**__== >> >>Justin A. Lemkul >>Ph.D. Candidate >>ICTAS Doctoral Scholar >>MILES-IGERT Trainee >>Department of Biochemistry >>Virginia Tech >>Blacksburg, VA >>jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080 >> >> >> >> http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justin<http://vt.edu/Pages/Personal/justin> >> >> <http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> >> > >> >>==**__== >>-- gmx-users mailing listgmx-users@gromacs.org >><mailto:gmx-users@gromacs.org> >> >> >> http://lists.gromacs.org/__**mailman/listinfo/gmx-users<http://lists.gromacs.org/__mailman/listinfo/gmx-users> >> >> <http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >> > >>Please search the archive at >> >> http://www.gromacs.org/__**Support/Mailing_Lists/Search<http://www.gromacs.org/__Support/Mailing_Lists/Search> >> >> <http://www.gromacs.org/**Support/Mailing_Lists/Search<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 >><mailto:gmx-users-request@**gromacs.org >> >. >> >>Can't post? Read >> http://www.gromacs.org/__**Support/Mailing_Lists<http://www.gromacs.org/__Support/Mailing_Lists> >> >> <http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >> > >> >> >> >> >> -- >> Best, >> Liang Liu >> > > -- > ==**== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==**== > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> > -- Best, Liang Liu -- 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] REMD problem
Does that mean I have to use MPI? I got an error "mdrun -multi is not supported with the thread library.Please compile GROMACS with MPI support" after run "mdrun -s md.tpr -multi 10 -replex 10" On Wed, Sep 28, 2011 at 12:58 PM, Justin A. Lemkul wrote: > > > Liu, Liang wrote: > >> Hi everyone, >> I tried to use Gromacs to run REMD simulation. >> Firstly a set of (md#).mdp file are make and the grompp command can >> generate the same amount of (md#).tpr file. >> Assume # = 10, >> then I tried to run REMD as mdrun -s md.tpr -np 10 -replex 10. >> >> However, a fetal error shows as "Need at least two replicas for replica >> exchange (option -multi)", what is this for? Thanks. >> >> >> > You have to use the -multi flag. Otherwise all mdrun does is run md.tpr > and try to do REMD with nothing. > > http://www.gromacs.org/**Documentation/How-tos/REMD#**Execution_Steps<http://www.gromacs.org/Documentation/How-tos/REMD#Execution_Steps> > > -Justin > > -- > ==**== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==**== > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> > -- Best, Liang Liu -- 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] REMD problem
Hi everyone, I tried to use Gromacs to run REMD simulation. Firstly a set of (md#).mdp file are make and the grompp command can generate the same amount of (md#).tpr file. Assume # = 10, then I tried to run REMD as mdrun -s md.tpr -np 10 -replex 10. However, a fetal error shows as "Need at least two replicas for replica exchange (option -multi)", what is this for? Thanks. -- Best, Liang Liu -- 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] simulation with position constraint by a harmonic potential
Liu, Liang wrote: >* > Thanks.*>* >*>* > Is this position restraint same to the >one "Position Restrained*>* MD". I*>* > see some tutorial shows there >are always three step to perform a*>* > simulation: Energy minimization, >Position Restrained MD and MD*>* Simulation.*>* *>* "Always" is too >strong, but this is common.*>* *>* > Is it possible to fulfill the >position restraint during Position*>* > Restrained MD? Thanks.*>* *>* >Yes, hence the name. How well they can be fulfilled depends on the*>* >initial and simulation conditions.*>* *>* *>* Thanks for this information.*>* >But how to perform a harmonic potential to all the heavy atoms of RNA?*>* >Justin said this one should be adjusted in the posre.itp file, and what *>* I >see in the file is all 1000. Does this means k=1000 in the equation of *>* E = >k (r-r0)^2?* Yes. See my previous message. I explained the contents of the file, which are also discussed in the manual. -Justin --- perfect, thanks a lot. Does this conflict with the bond restraint, e.g. LINCS algorithm, during simulation? -- Best, Liang Liu -- 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] simulation with position constraint by a harmonic potential
It is weird why I always receive the digest of the mailing list but the specific topic? On Tue, Sep 27, 2011 at 9:14 AM, Liu, Liang wrote: > > Thanks. >> > >> > Is this position restraint same to the one "Position Restrained MD". I >> > see some tutorial shows there are always three step to perform a >> > simulation: Energy minimization, Position Restrained MD and MD >> Simulation. >> >> "Always" is too strong, but this is common. >> >> >> > Is it possible to fulfill the position restraint during Position >> > Restrained MD? Thanks. >> >> Yes, hence the name. How well they can be fulfilled depends on the >> initial and simulation conditions. >> > > Thanks for this information. > But how to perform a harmonic potential to all the heavy atoms of RNA? > Justin said this one should be adjusted in the posre.itp file, and what I > see in the file is all 1000. Does this means k=1000 in the equation of E = k > (r-r0)^2? > Thanks. > > >> >> Mark >> > > -- > Best, > Liang Liu > -- Best, Liang Liu -- 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] simulation with position constraint by a harmonic potential
> > > Thanks. > > > > Is this position restraint same to the one "Position Restrained MD". I > > see some tutorial shows there are always three step to perform a > > simulation: Energy minimization, Position Restrained MD and MD > Simulation. > > "Always" is too strong, but this is common. > > > Is it possible to fulfill the position restraint during Position > > Restrained MD? Thanks. > > Yes, hence the name. How well they can be fulfilled depends on the > initial and simulation conditions. > Thanks for this information. But how to perform a harmonic potential to all the heavy atoms of RNA? Justin said this one should be adjusted in the posre.itp file, and what I see in the file is all 1000. Does this means k=1000 in the equation of E = k (r-r0)^2? Thanks. > > Mark > -- Best, Liang Liu -- 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] simulation with position constraint by a harmonic potential
Thanks. Is this position restraint same to the one "Position Restrained MD". I see some tutorial shows there are always three step to perform a simulation: Energy minimization, Position Restrained MD and MD Simulation. Is it possible to fulfill the position restraint during Position Restrained MD? Thanks. On Mon, Sep 26, 2011 at 4:56 PM, Justin A. Lemkul wrote: > > > Liu, Liang wrote: > >> Firstly I want to thank for your reply, yes, it should be position >> restraint. >> >> I don't know how to reply in the thread, actually that was my first post. >> Therefore I have to ask you here, hope it also work to you. >> >> > Simply reply to the message. The discussion needs to stay on the list. > The members are not private tutors. > > My question is how to perform a position restraint simulation with the >> heavy atom constrained to its initial position by a harmonic potential >> E=k(r-r0)^2, >> which changes with k equal to 0, 10, 20, ..., 90, 100, and so on? >> >> > You can adjust the force constant in the posre.itp file. There is no > automated way of decreasing or increasing a restraint; independent > simulations must be run on the different topologies. > > -Justin > > Thanks, and any helps will be highly appreciated. >> >> -- >> Best, >> Liang Liu >> > > -- > ==**== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==**== > -- Best, Liang Liu -- 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] simulation with position constraint by a harmonic potential
00 222 1 1000 1000 1000 223 1 1000 1000 1000 224 1 1000 1000 1000 227 1 1000 1000 1000 229 1 1000 1000 1000 230 1 1000 1000 1000 232 1 1000 1000 1000 233 1 1000 1000 1000 235 1 1000 1000 1000 236 1 1000 1000 1000 237 1 1000 1000 1000 238 1 1000 1000 1000 241 1 1000 1000 1000 242 1 1000 1000 1000 244 1 1000 1000 1000 245 1 1000 1000 1000 246 1 1000 1000 1000 248 1 1000 1000 1000 250 1 1000 1000 1000 252 1 1000 1000 1000 253 1 1000 1000 1000 254 1 1000 1000 1000 255 1 1000 1000 1000 256 1 1000 1000 1000 257 1 1000 1000 1000 260 1 1000 1000 1000 262 1 1000 1000 1000 263 1 1000 1000 1000 265 1 1000 1000 1000 266 1 1000 1000 1000 268 1 1000 1000 1000 269 1 1000 1000 1000 270 1 1000 1000 1000 271 1 1000 1000 1000 274 1 1000 1000 1000 275 1 1000 1000 1000 277 1 1000 1000 1000 278 1 1000 1000 1000 279 1 1000 1000 1000 281 1 1000 1000 1000 283 1 1000 1000 1000 285 1 1000 1000 1000 286 1 1000 1000 1000 287 1 1000 1000 1000 288 1 1000 1000 1000 289 1 1000 1000 1000 290 1 1000 1000 1000 293 1 1000 1000 1000 295 1 1000 1000 1000 296 1 1000 1000 1000 298 1 1000 1000 1000 299 1 1000 1000 1000 301 1 1000 1000 1000 302 1 1000 1000 1000 303 1 1000 1000 1000 304 1 1000 1000 1000 305 1 1000 1000 1000 307 1 1000 1000 1000 308 1 1000 1000 1000 311 1 1000 1000 1000 312 1 1000 1000 1000 313 1 1000 1000 1000 315 1 1000 1000 1000 317 1 1000 1000 1000 319 1 1000 1000 1000 320 1 1000 1000 1000 321 1 1000 1000 1000 322 1 1000 1000 1000 323 1 1000 1000 1000 324 1 1000 1000 1000 327 1 1000 1000 1000 329 1 1000 1000 1000 330 1 1000 1000 1000 332 1 1000 1000 1000 333 1 1000 1000 1000 335 1 1000 1000 1000 337 1 1000 1000 1000 338 1 1000 1000 1000 341 1 1000 1000 1000 342 1 1000 1000 1000 343 1 1000 1000 1000 344 1 1000 1000 1000 346 1 1000 1000 1000 348 1 1000 1000 1000 350 1 1000 1000 1000 351 1 1000 1000 1000 352 1 1000 1000 1000 353 1 1000 1000 1000 354 1 1000 1000 1000 355 1 1000 1000 1000 358 1 1000 1000 1000 360 1 1000 1000 1000 361 1 1000 1000 1000 363 1 1000 1000 1000 364 1 1000 1000 1000 366 1 1000 1000 1000 367 1 1000 1000 1000 368 1 1000 1000 1000 369 1 1000 1000 1000 372 1 1000 1000 1000 373 1 1000 1000 1000 375 1 1000 1000 1000 376 1 1000 1000 1000 377 1 1000 1000 1000 379 1 1000 1000 1000 381 1 1000 1000 1000 383 1 1000 1000 1000 384 1 1000 1000 1000 385 1 1000 1000 1000 386 1 1000 1000 1000 387 1 1000 1000 1000 388 1 1000 1000 1000 391 1 1000 1000 1000 393 1 1000 1000 1000 394 1 1000 1000 1000 396 1 1000 1000 1000 397 1 1000 1000 1000 399 1 1000 1000 1000 401 1 1000 1000 1000 402 1 1000 1000 1000 403 1 1000 1000 1000 405 1 1000 1000 1000 406 1 1000 1000 1000 407 1 1000 1000 1000 409 1 1000 1000 1000 411 1 1000 1000 1000 413 1 1000 1000 1000 So how to adjust the force constraint to the harmonic poteitial E = k(r-r0)^2, with different values of k? I am totally a new user of Gromacs, even MD simulation. Please help, Thanks a lot. On Mon, Sep 26, 2011 at 4:56 PM, Justin A. Lemkul wrote: > > > Liu, Liang wrote: > >> Firstly I want to thank for your reply, yes, it should be position >> restraint. >> >> I don't know how to reply in the thread, actually that was my first post. >> Therefore I have to ask you here, hope it also work to you. >> >> > Simply reply to the message. The discussion needs to stay on the list. > The members are not private tutors. > > My question is how to perform a position restraint simulation with the >> heavy atom constrained to its initial position by a harmonic potential >> E=k(r-r0)^2, >> which changes with k equal to 0, 10, 20, ..., 90, 100, and so on? >> >> > You can adjust the force constant in the posre.itp file. There is no > automated w
[gmx-users] simulation with position constraint by a harmonic potential
I am running Gromacs for RNAs, and I got a problem during the simulation: How to perform the simulation with each heavy atom constrained to its initial position by a harmonic potential, E = k(r-r0)^2? -- Best, Liang Liu -- 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] unexpexted stop of simulation
Dear all, I'm performing a three-day simulation. It runs well for the first day, but stops for the second one. The error message is below. Does anyone know what might be the problem? Thanks Liang Program mdrun, VERSION 4.5.1-dev-20101008-e2cbc-dirty Source code file: /home/z8g/download/gromacs.head/src/gmxlib/checkpoint.c, line: 1748 Fatal error: Failed to lock: md100ns.log. Already running simulation? For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- "Sitting on a rooftop watching molecules collide" (A Camp) Error on node 0, will try to stop all the nodes Halting parallel program mdrun on CPU 0 out of 32 gcq#348: "Sitting on a rooftop watching molecules collide" (A Camp) -- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode -1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -- [node139:04470] [[37327,0],0]-[[37327,1],0] mca_oob_tcp_msg_recv: readv failed: Connection reset by peer (104) -- mpiexec has exited due to process rank 0 with PID 4471 on node node139 exiting without calling "finalize". This may have caused other processes in the application to be terminated by signals sent by mpiexec (as reported here). -- 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] who has the force field file of gromos45a4
Dear all, Right now I plan to use the Gromos 45a4 force field to perform a simulation of carbohydrates. However, this force field is absent from the version of Gromacs (both Gomacs v4.0.7 and v 4.5.1) I'm using. If some one has this force field files, could you, please, pass to me? Best, Liang-- 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] coordinate file (PDB file) of cellobiose
Dear all, Right now I plan to conduct a MD on Cellobiose. Is there anyone who has the coordinate files of alpha and beta cellobiose (including hydrogen atoms)? Could you, please, forward to me? Sincerely, Liang-- 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] Gromos 45A4
Dear all, I have seen people using Gromos 45A4 force field to simulate sugars in Gromacs. But there is no such force field in the version 4.07 I'm using now. Where can I find the 45A4 force field? Or use some other force filed to replace it? sincerely, Liang-- 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] How to choose lipid molecules?
Dear all, I am a freshman to membrane protein simulation, and i was wondering how to choose lipid molecules for my system. As we know, there are lots of lipid molecules: DMPC, DPPC, POPE. but how do people decide that which type of lipid to use? and what kinds of criteria should we follow? Thanks so much! Liang___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: how to write the correct top file for membrane protein
Hi Mark, i indeed checked some publications about how to choose lipid force field, please check this reference: Journal of Physics: Condensed Matter 18(2006) S1221-S1234, Tieleman and his coworkers tested two combinations: Berger+ffgmx+SPC, Berger+OPLS+TIP4P, and they recommended that using OPLS together with united-atom lipid force field. So, i would like to know whether it is reasonable or not, and how should i modify them in top file? Thanks for your reply. Liang - Original Message - From: <[EMAIL PROTECTED]> To: Sent: Monday, November 26, 2007 5:28 PM Subject: gmx-users Digest, Vol 43, Issue 96 Message: 4 Date: Mon, 26 Nov 2007 12:24:31 +0800 From: Mark Abraham <[EMAIL PROTECTED]> Subject: Re: [gmx-users] Re: how to write the correct top file for membrane protein To: Discussion list for GROMACS users Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset=ISO-8859-1; format=flowed liang wrote: Dear Mark, Thanks for your advice, but from my understanding, Berger's force field is based on OPLS/Amber. Lipid itp files from Tieleman's website just use the atom type definitions from GROMOS87. And GROMOS87 is out of fashion now. So thats why i think it would be better to use OPLS for protein and "ffgmx.itp" for lipid. Fine, but you can't use them both at the same time (unless you want to produce indefensible gibberish), and ffgmx is deprecated anyway. I am not sure whether I misunderstand the usage of Berger's force field, if i am wrong, please give me further instruction. See my advice last time. Don't mix forcefields unless you already have hard evidence that this combination works - and I'm not aware of any. The link Justin provided warns you about that. You need to find a force field that has parameters optimized that suit your system. Mixing anything else is about 99% likely to make an expensive (and poor) random number generator. Look in the literature for systems similar to yours and see if their ideas on force fields are suitable for you to use. Making it up based on stuff you found on the web is for high school students doing assignments :-) Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: how to write the correct top file for membrane protein
Dear Mark, Thanks for your advice, but from my understanding, Berger's force field is based on OPLS/Amber. Lipid itp files from Tieleman's website just use the atom type definitions from GROMOS87. And GROMOS87 is out of fashion now. So thats why i think it would be better to use OPLS for protein and "ffgmx.itp" for lipids. I am not sure whether I misunderstand the usage of Berger's force field, if i am wrong, please give me further instruction. I hope it would not be bothering you. Thanks so much! Liang Dear Justin, Thanks for you quickly reply. I have tried before to comment out the section of [ defaults ] in the next itp file, but still too many warnings and final crashed. And i think it would not be the best method to solve this problem, because i have to use ffgmx.itp to deal with DPPC. Is there any other method i can try? Don't mix forcefields unless you already have hard evidence that this combination works - and I'm not aware of any. The link Justin provided warns you about that. You need to find a force field that has parameters optimized that suit your system. Mixing anything else is about 99% likely to make an expensive (and poor) random number generator. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] how to write the correct top file for membraneprotein system?
Hi Hadas, i have tried to use gromos87 for protein, everything is ok. (just with ffgmx.itp) but if i use opls for protein, i have to add "ffoplsaa.itp" in top file, otherwise it cannot provide some parameters for protein. Did you use gromos87 to generate your protein itp files (chain_A .itp ...) ? Thanks Liang - Original Message - From: "Hadas Leonov" <[EMAIL PROTECTED]> To: "liang" <[EMAIL PROTECTED]>; "Discussion list for GROMACS users" Sent: Sunday, November 25, 2007 5:26 PM Subject: Re: [gmx-users] how to write the correct top file for membraneprotein system? > Hi Liang, > > Do you have to define ffoplsaa.itp in your top file? isn't it enough to > generate your protein topology with the OPLS forcefield using pdb2gmx and > include the protein's generated itp files? > > I don't use OPLS, but my own definition of the .top file goes like this: > > ; generic + lipid topology > #include "ffgmx.itp" > #include "lipid.itp" > #include "dmpc.itp" > #include "ions.itp" > > ; protein > #include "chain_A.itp" > #include "chain_B.itp" > #include "chain_C.itp" > #include "chain_D.itp" > > ; water > #include "spc.itp" > > Rest of my molecule definitions are similar (protein first, then lipid, then > water, and finally ions to neutralize the system). > > Hope it helps, > Hadas. > - Original Message - > From: "liang" <[EMAIL PROTECTED]> > To: "Justin A. Lemkul" <[EMAIL PROTECTED]> > Cc: > Sent: Sunday, November 25, 2007 7:41 AM > Subject: Re: [gmx-users] how to write the correct top file for > membraneprotein system? > > >> Dear Justin, >> >> Thanks for you quickly reply. >> >> I have tried before to comment out the section of [ defaults ] in the next >> itp file, but still too many warnings and final crashed. >> And i think it would not be the best method to solve this problem, because >> i have to use ffgmx.itp to deal with DPPC. >> >> Is there any other method i can try? >> >> Thanks >> >> Liang >> >> - Original Message - >> From: "Justin A. Lemkul" <[EMAIL PROTECTED]> >> To: "liang" <[EMAIL PROTECTED]>; "Discussion list for GROMACS >> users" >> Sent: Sunday, November 25, 2007 12:23 PM >> Subject: Re: [gmx-users] how to write the correct top file for membrane >> protein system? >> >> >>> Quoting liang <[EMAIL PROTECTED]>: >>> >>>> Dear User, >>>> >>>> i try to perform simulation on membrane protein ( proterin + DPPC ). >>>> And i use OPLS for protein, Berger force field for DPPC. >>>> But after i construct this system, i cannot obtain tpr file by using >>>> grompp. >>>> >>>> Here is my topol.top : >>>> >>>> ; protein >>>> #include "ffoplsaa.itp" >>>> #include "protein-opls.itp" >>>> >>>> ; membrane >>>> #include "ffgmx.itp" >>>> #include "lipid.itp" >>>> #include "dppc.itp" >>>> >>>> ; Include water topology >>>> #include "spc.itp" >>>> >>>> [ system ] >>>> ; name >>>> Membrane in water >>>> >>>> [ molecules ] >>>> ; name number >>>> Protein1 >>>> DPPC 123 >>>> SOL 14189 >>>> >>>> here is the result: >>>> >>> >>>> Fatal error: >>>> Invalid order for directive defaults, file >>>> ""/home/gmx331/share/gromacs/top/ffgmx.itp"", line 4 >>>> >>> >>> >>> I suspect it is a result of using two different force fields. The [ >>> defaults ] >>> will be defined in the first force field (in your case, ffoplsaa.itp), >>> but then >>> grompp is finding a second [ defaults ] in ffgmx.itp. See here: >>> >>> http://wiki.gromacs.org/index.php/Errors#Found_a_second_defaults_directive_file >>> >>> -Justin >>> >>>> >>>> Could you please give me some suggestion? i appreciate y
Re: [gmx-users] how to write the correct top file for membrane protein system?
Dear Justin, Thanks for you quickly reply. I have tried before to comment out the section of [ defaults ] in the next itp file, but still too many warnings and final crashed. And i think it would not be the best method to solve this problem, because i have to use ffgmx.itp to deal with DPPC. Is there any other method i can try? Thanks Liang - Original Message - From: "Justin A. Lemkul" <[EMAIL PROTECTED]> To: "liang" <[EMAIL PROTECTED]>; "Discussion list for GROMACS users" Sent: Sunday, November 25, 2007 12:23 PM Subject: Re: [gmx-users] how to write the correct top file for membrane protein system? Quoting liang <[EMAIL PROTECTED]>: Dear User, i try to perform simulation on membrane protein ( proterin + DPPC ). And i use OPLS for protein, Berger force field for DPPC. But after i construct this system, i cannot obtain tpr file by using grompp. Here is my topol.top : ; protein #include "ffoplsaa.itp" #include "protein-opls.itp" ; membrane #include "ffgmx.itp" #include "lipid.itp" #include "dppc.itp" ; Include water topology #include "spc.itp" [ system ] ; name Membrane in water [ molecules ] ; name number Protein1 DPPC 123 SOL 14189 here is the result: Fatal error: Invalid order for directive defaults, file ""/home/gmx331/share/gromacs/top/ffgmx.itp"", line 4 I suspect it is a result of using two different force fields. The [ defaults ] will be defined in the first force field (in your case, ffoplsaa.itp), but then grompp is finding a second [ defaults ] in ffgmx.itp. See here: http://wiki.gromacs.org/index.php/Errors#Found_a_second_defaults_directive_file -Justin Could you please give me some suggestion? i appreciate your help. Thanks so much! Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] how to write the correct top file for membrane protein system?
Dear User, i try to perform simulation on membrane protein ( proterin + DPPC ). And i use OPLS for protein, Berger force field for DPPC. But after i construct this system, i cannot obtain tpr file by using grompp. Here is my topol.top : ; protein #include "ffoplsaa.itp" #include "protein-opls.itp" ; membrane #include "ffgmx.itp" #include "lipid.itp" #include "dppc.itp" ; Include water topology #include "spc.itp" [ system ] ; name Membrane in water [ molecules ] ; name number Protein1 DPPC 123 SOL 14189 here is the result: Fatal error: Invalid order for directive defaults, file ""/home/gmx331/share/gromacs/top/ffgmx.itp"", line 4 Could you please give me some suggestion? i appreciate your help. Thanks so much!___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] How to add calcium ions at desired position?
> Never couple solvent and ions separately. Check out: > http://wiki.gromacs.org/index.php/Thermostats > Try tc-grps = Protein Non-protein excuse me, if the system includes lipid bilayer, how should i set the tc-prgs? Protein + Lipids + Sol and Ion? or Protein + Non-protein ? thanks___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: about gromacs-osx-intel-3.3.1.dmg
Dear Users, actually, libXm.2.dylib is missing. Could anyboby tell me how to get this file? Thanks >liang wrote: >> Dear Users, >> >> i would like to install gromacs on Mac OSX tiger 10.4.10, and i download >> this dmg file from ftp site. >> after i installed successfully, i tried to test some commands >> but it showed some warnings: >> >> dyld: Library not loaded: /usr/local/gromacs/lib/libmd.4.dylib >does this library exist? Or did you put it in another directory? >>Referenced from: /Users/Wayne/Gromacs/bin/mdrun >>Reason: image not found >> Trace/BPT trap >> >> it seems to lack a lib file, but i dont know how to get it. >> does anyone give me some advice? >> >> Thanks so much !!! ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] about gromacs-osx-intel-3.3.1.dmg
Dear Users, i would like to install gromacs on Mac OSX tiger 10.4.10, and i download this dmg file from ftp site. after i installed successfully, i tried to test some commands but it showed some warnings: dyld: Library not loaded: /usr/local/gromacs/lib/libmd.4.dylib Referenced from: /Users/Wayne/Gromacs/bin/mdrun Reason: image not found Trace/BPT trap it seems to lack a lib file, but i dont know how to get it. does anyone give me some advice? Thanks so much !!! ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] rhdo box shape changed during simulation
Hi Tsjerk, Thanks for the hint. :-) I will check the compatability of isotropic scaling and parinello-rahman method. Thanks!LiangOn 11/2/06, Tsjerk Wassenaar <[EMAIL PROTECTED]> wrote: Hi Liang,I'm not completely sure on this one, but isn't parinello-rahman perdefinition anisotropic? Check the manual.Regarding the second question, my usual answer is "there's no suchthing as a box in the infinite simulation system". There's only the lattice, which is defined by three vectors. But whether the shape ofthe unit cell is allowed to change depends on the pressure couplingyou use. When using isotropic pressure coupling you're using a scalarto scale the box vectors and your box shape (the angles between your vectors and the relative lengths) will be retained. But if I recallcorrectly, parinello-rahman works by changing the box vectors based onthe "velocities" of these box vectors, which are scaled at every step to relax to the desired pressure. Thus, anisotropic pressure scaling.You could try to use Berendsen pressure coupling.Best,TsjerkOn 11/2/06, Liang Ma < [EMAIL PROTECTED]> wrote:> Hi Tsjerk,> Thanks for you fast reply. :-):-) Yes, I indeed used the isotropic> pressure scaling method. That's why I found it's surpring that one> dimension of my system actually shrinked. Is there any other possible reason > for this? Or, is there any constraint to keep the box shape always> rhdo-like? If not, does gromacs always treat rhdo as triclinic and the box> shaple actually is free to change?>> > Thanks a lot!>> Liang>> This is my grompp file:>> ; title and include files> title= salt> cpp = cpp> include = > -I/home/ma/gromacs/share/gromacs/top -I./> define => ; integrator and input/output setting up> integrator = md> nsteps = 60 ; 1.2 ns equilibration > dt = 0.002> nstxout = 5000> nstvout = 5000> nstenergy= 500> nstxtcout= 500> nstlog = 500 > xtc_grps = System> energygrps = System> comm_mode= none> ; neighbor searching and vdw/pme setting up> nstlist = 10> ns_type = grid > pbc = xyz> rlist= 1.4>> coulombtype = pme> fourierspacing = 0.1> pme_order= 6> rcoulomb = 1.4>> vdwtype = switch> rvdw_switch = 1.0> rvdw = 1.2>> ; cpt control> tcoupl = nose-hoover> tc-grps = System > tau_t= 0.1> ref_t= 300> Pcoupl = parrinello-rahman> pcoupltype = isotropic> tau_p= 1.0> compressibility = 4.5e-5> ref_p= 1.0>> ; velocity & temperature control> gen_vel = no> gen_temp = 300> annealing= no> constraints = hbonds > constraint_algorithm = shake> morse= no>>>>> On 11/2/06, Tsjerk Wassenaar < [EMAIL PROTECTED]> wrote: > >> > Hi Liang,> >> > Apparently, your system contracted in one direction. You can avoid> > this by simulating at constant volume or by using isotropic pressure> > coupling. > > Your protein should not have direct interactions with its periodic> > images during the simulation. This usually means you can discard your> > results.> > The last two values are the x and y skewing of the third vector > > defining your periodic lattice (the periodic boundary conditions).> > Likewise, the first two zeros are the y and z skewing of the first> > vector and the other two zeros are the x and z skewing of the second > > vector. You can check chapter 3 of the gromacs manual to get to know> > more about periodic boundary conditions in gromacs.> >> > Best,> >> > Tsjerk> > > > On 11/2/06, Liang Ma <[EMAIL PROTECTED]> wrote:> > > Hi all gromacs users,> > > I am simulating a protein in explicit solvent with Periodic > boundary> > > condition and PME . The box type I used> > > is rhdo (rhombic dodecahedron). However, I checked the box length and> angle> > > during simulations, it deviates far away from the normal rhdo box > shape.> > > For example, the third line in pdb at the beginning is :> > > CRYST1 90.093 90.093 90.093 60.00 60.00 90.00 P 1 1
Re: [gmx-users] rhdo box shape changed during simulation
Hi Tsjerk, Thanks for you fast reply. :-):-) Yes, I indeed used the isotropic pressure scaling method. That's why I found it's surpring that one dimension of my system actually shrinked. Is there any other possible reason for this? Or, is there any constraint to keep the box shape always rhdo-like? If not, does gromacs always treat rhdo as triclinic and the box shaple actually is free to change? Thanks a lot! LiangThis is my grompp file:; title and include filestitle = saltcpp = cppinclude = -I/home/ma/gromacs/share/gromacs/top -I./ define =; integrator and input/output setting upintegrator = mdnsteps = 60 ; 1.2 ns equilibrationdt = 0.002nstxout = 5000 nstvout = 5000nstenergy = 500nstxtcout = 500nstlog = 500xtc_grps = Systemenergygrps = Systemcomm_mode = none ; neighbor searching and vdw/pme setting upnstlist = 10ns_type = gridpbc = xyzrlist = 1.4coulombtype = pme fourierspacing = 0.1pme_order = 6rcoulomb = 1.4vdwtype = switchrvdw_switch = 1.0rvdw = 1.2; cpt control tcoupl = nose-hoovertc-grps = Systemtau_t = 0.1ref_t = 300Pcoupl = parrinello-rahmanpcoupltype = isotropic tau_p = 1.0compressibility = 4.5e-5ref_p = 1.0; velocity & temperature controlgen_vel = nogen_temp = 300annealing = no constraints = hbondsconstraint_algorithm = shakemorse = noOn 11/2/06, Tsjerk Wassenaar < [EMAIL PROTECTED]> wrote:Hi Liang,Apparently, your system contracted in one direction. You can avoid this by simulating at constant volume or by using isotropic pressurecoupling.Your protein should not have direct interactions with its periodicimages during the simulation. This usually means you can discard your results.The last two values are the x and y skewing of the third vectordefining your periodic lattice (the periodic boundary conditions).Likewise, the first two zeros are the y and z skewing of the first vector and the other two zeros are the x and z skewing of the secondvector. You can check chapter 3 of the gromacs manual to get to knowmore about periodic boundary conditions in gromacs.Best,Tsjerk On 11/2/06, Liang Ma <[EMAIL PROTECTED]> wrote:> Hi all gromacs users,> I am simulating a protein in explicit solvent with Periodic boundary > condition and PME . The box type I used> is rhdo (rhombic dodecahedron). However, I checked the box length and angle> during simulations, it deviates far away from the normal rhdo box shape.> For example, the third line in pdb at the beginning is : > CRYST1 90.093 90.093 90.093 60.00 60.00 90.00 P 1 1> which is a perfect rhdo box.>> During the simulation, it changed to:> CRYST1 89.503 89.503 68.425 105.59 105.59 90.00 P 1 1> ,which is not rhdo.> Meanwhile, the distance between the protein and its nearst image decreased> dramatically, (they even touched).> So my question is this normal? If not, is there any way to constraint the > box always in a rhdo box shape (a=b=c)>> And also,> the last line in the gro file changed to:> 8.95030 8.95030 6.32914 0.0 0.0 0.0 0.0> -1.83879 -1.83879 > what does the last two negative values exactly mean?>>> Thanks for any help!> Liang>> ___> gmx-users mailing list gmx-users@gromacs.org> http://www.gromacs.org/mailman/listinfo/gmx-users> Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED].> Can't post? Read> http://www.gromacs.org/mailing_lists/users.php >>--Tsjerk A. Wassenaar, Ph.D.post-docNMR, Utrecht University,Padualaan 8,3584 CH Utrecht, the NetherlandsP: +31-30-2539931F: +31-30-2537623___ gmx-users mailing listgmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED].Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] rhdo box shape changed during simulation
Hi all gromacs users, I am simulating a protein in explicit solvent with Periodic boundary condition and PME . The box type I used is rhdo (rhombic dodecahedron). However, I checked the box length and angle during simulations, it deviates far away from the normal rhdo box shape. For example, the third line in pdb at the beginning is : CRYST1 90.093 90.093 90.093 60.00 60.00 90.00 P 1 1which is a perfect rhdo box. During the simulation, it changed to:CRYST1 89.503 89.503 68.425 105.59 105.59 90.00 P 1 1 ,which is not rhdo. Meanwhile, the distance between the protein and its nearst image decreased dramatically, (they even touched).So my question is this normal? If not, is there any way to constraint the box always in a rhdo box shape (a=b=c) And also, the last line in the gro file changed to:8.95030 8.95030 6.32914 0.0 0.0 0.0 0.0 -1.83879 -1.83879what does the last two negative values exactly mean? Thanks for any help!Liang ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] a problem about Coul-LR in energy groups output. Coul-LR is always ZERO !
I want to analyze the energy during a normal simulation. Some strange things happened. In mdp file, I selected DNA, NA+, SOL for energy groups output. When I analyzed edr file by g_energy, I found Coul_LR is always ZERO. I think my parameters have no problem, rlist = 1.0 rcoulomb = 1.0, rvdw = 1.0. Furthermore, when I selected 'System' for energy output, Coul_LR have some reasonable values. When I do MD simulation in other computer, there is NO output for Coul-LR with the SAME parameter file. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: problem with dimer simulation !
hi cw,using trjconv -pbc nojump should remove the jumps. then you can analyse interactions between different chains, while it doesn't matter for the analysis where they diffuse.daniela hello, daniela thanks for your reply, it really doesn't matter when i calculate the distance between two peptides ? best regards, Liang ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: problem with dimer simulation !
try - cluster, and then as cluster group protein.Kay. hello, Kay thanks so much for your advice, but with -pbc cluster, one of the two peptides still move out of the box and frequently jump back. i have no idea about it, any else should i do ? best regards, Liang ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] problem with dimer simulation !
hi, all user: i performed the dimer simulation, and want to realize the interaction between two peptides. but frequently, i encountered this kind of problem: sometimes peptides moved out of the box, and sometimes they jumped back. i have tried so many way to pull them back with trjconv command, but still cause some unexpected problem. for example, peptides break to many parts ( with -pbc whole ) or diffuse out of box gradually ( with -pbc nojump ) with -ur or -center still not the trajectory i really want. i think maybe there are some tricks to perform. any suggestions for me ? thanks sooo much! ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: freeenergy calculation
Date: Thu, 01 Jun 2006 15:34:14 +0530 From: "lalitha selvam" <[EMAIL PROTECTED]> Subject: [gmx-users] freeenergy calculation To: gmx-users@gromacs.org Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; format=flowed i have completed my simulation.i want to analyse my protein.can u help me how to calculate the free binding energy calculation,which program i should use.i've read gromacs manual 3.3 but i'm in need of any other new analysis are included in version 3.3 or not.so where can i getthe information on availability of more analysis in GROMACS 3.3 version comapred to older version. thanks sir.i'm in hurry.Plz anyone help me. hello, you can use g_sham program (new one in 3.3)to calculate free energy distribution and draw the picture. first, you should prepare a xvg file with three columns. the first is frame time, the second and third are the parameters you want to calculate, for example like this: Time RMSD dist 0 1.2 0.8 1 1.3 1.1 2 0.5 0.9 . . . . . . and then, use the following command: g_sham -f *.xvg -ls you can get the pic, and with -ngrid you can get the high resolution pics. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] how to use g_sham ?
Liang wrote: Dear all users : g_sham is a new program in 3.3 and i cant find any discussion about how to use in mailing lists, and i didnt catch the point about the instructions in user manual. Is it possible to draw pics about PMF or free energy landscape using some special coordinates, like RMSD, potential, or dihedral angle variations etc. ? all yes. have you run g_sham -h ? YES, g_sham -h is the same as user manual, but i still have some puzzle. for example, i wanna calculate the RMSD vary with potential energy, so i generate rmsd.xvg and energy.xvg. g_sham -f rmsd.xvg -ene energy.xvg is it right? and how to set up the parameter of free energy landscape vectors? like -dim -ngrid -xmin -xmax -gmax THANKS SO MUCH !! ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] how to use g_sham ?
Dear all users : g_sham is a new program in 3.3 and i cant find any discussion about how to use in mailing lists, and i didnt catch the point about the instructions in user manual. Is it possible to draw pics about PMF or free energy landscape using some special coordinates, like RMSD, potential, or dihedral angle variations etc. ? and How to set up the parameters to get a sensible picture? thanks so much for any reply ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
