Re: [gmx-users] سلام استاد
salam, man mishnasametun? mozoe naghashie chiye? 2012/5/2 Shima Arasteh > > سلام > یه خواهش دارم. من بعد قاب کردن نقاشی، ازش عکس نگرفتم. لطفا اگر تونستین > برام چندتا عکس خوب بگیرین > مرسی > میشه لطفا؟ > > > > -- > 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
[gmx-users] compute displacement
I have performed a MD simulation with gromacs 4.0.7 the system that I have simulated contain 1000 atomes and now in order to compute intermediate scattering function F(q,t)=1/N<∑_(i=1)^N〖exp(-iq.(r_i (t)-r_(i(0))> I need to compute (ri (t)-ri(0)) for all atomes and all times. how can I do this? mean square of this term gives us mean square displacment and the gromacs can do it by using g_msd is there any command that give us .(ri(t)-ri(0)) and not mean squre of it? -- 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] compute displacement
I have performed a MD simulation with gromacs 4.0.7 the system that I have simulated contain 1000 atomes and now in order to compute intermediate scattering function F(q,t)=1/N<∑_(i=1)^N〖exp(-iq.(r_i (t)-r_(i(0))> I need to compute (ri (t)-ri(0)) for all atomes and all times. how can I do this? mean square of this term gives us mean square displacment and the gromacs can do it by using g_msd is there any command that give us .(ri (t)-ri(0)) and not mean squre of it? -- 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] Fwd: genbox
I have .gro and .top of a nanoparticle at temperature 1K and I want to add the simulation box some other atoms at temperature 300K. is there any body knows how can I do it. I have used (genbox -cp nanoparticle.gro -ci otheratom.gro -p nanoparticle.top -o out) but it add more than atoms than I expect for example if there is 600 other atoms in otheratom,gro file this command add 2000 atoms to simulation box and also nanoparticle.top does not update. thanks in advance -- 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] genbox
I have .gro and .top of a nanoparticle at temperature 1K and I want to add the simulation box some other atomes at temperature 300K. is there any body knows how can I do it. I have used (genbox -cp nanoparticle.gro -ci otheratom.gro -p nanoparticle.top -o out) but it add more than atomes than I expect for example if there is 600 other atomes in otheratom,gro file this command add 2000 atomes to simulation box and also nanoparticle.top does not update. thanks in advance -- 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] problem with gromcas 4.5.3
I have installed gromacs version 4.5.3. when I want to use pdb2gmx for generating .top and .gro files for 1000 argon atoms, in topology file I have seen another atom O with mass 1.48594e-41 as below I do not know what to do.I do not confront with such problems when I had 4.0.7 version of gromacs. please help me. also I have used gromos43a1 force feild. [ moleculetype ] ; Namenrexcl Other_chain_A 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeBchargeB massB ; residue 1 GAS rtp GAS q 0.0 1 AR 1GAS AR 1 0 1 ; qtot 0 ; residue 2 GAS rtp GAS q 0.0 2 O 2GAS AR 2 0 1.48594e-41 ; qtot 0 ; residue 3 GAS rtp GAS q 0.0 3 O 3GAS AR 3 0 1.48594e-41 ; qtot 0 ; residue 4 GAS rtp GAS q 0.0 4 O 4GAS AR 4 0 1.48594e-41 ; qtot 0 ; residue 5 GAS rtp GAS q 0.0 5 O 5GAS AR 5 0 1.48594e-41 ; qtot 0 ; residue 6 GAS rtp GAS q 0.0 6 O 6GAS AR 6 0 1.48594e-41 ; qtot 0 ; residue 7 GAS rtp GAS q 0.0 -- 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] initial structures for md simulations
packmol and hyperchem can do it for u. On Wed, Feb 16, 2011 at 4:57 AM, Mark Abraham wrote: > On 16/02/2011 11:24 PM, oguz gurbulak wrote: > > *Dear All*, > > > > I want to generate some initial crystalline structures of my target molecules > for md simulations. *Are there any free softwares* to do this? > > > Some sources for obtaining initial coordinates can be found here > http://www.gromacs.org/Documentation/File_Formats/Coordinate_File. I doubt > there is going to be software to generate "crystalline" structures (whatever > you mean by that). You could get a structure and replicate it with (e.g. > genconf). > > > And are there any complete sources that give the theoretical structures > of organic molecules ( like hydrocarbons ) determined by the experiments > and give the x-ray, neutron scattering, NMR, IR or Raman results of organic > molecules apart from the articles ? Could you please share your thoughts > about this issue ? > > > Theoretical structures you compute according to some model. Experimental > data tends to live in original literature and lots of specialist databases. > Which do you actually want? Google is your friend either way. > > 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 > -- 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] Fwd: specific heat
I have performed an annealing simulation from temp 300 K to 0 K and I do not know how to use g_energy command in order to give me heat capacity Cv as a function of time or temperature. could anybody help me please? the version of gromacs that I have installed is 4-5-3 -- 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] specific heat
I have performed an annealing simulation from temp 300 K to 0 K and I do not know how to use g_energy command to give me heat capacity Cv as a function of time or temperature. could anybody help me please? the version of gromacs that I have installed is 4-5-3 -- 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] specific heat
is there any command in gromacs that gives me a list of data points for specific heat and suseptibility as a function of temperature or time ? if not, then how can i calculate specific heat or polt Cv as a fuction of T? -- 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] segmentation error
I managed to run my simulation but which kind of coulomtype can I use except PME? also I get different averages for kinetic and potential energies than before reducing units I think these numbers must be the same because E*=E/epsilon (epsilon is about 0.9977) for argon. could u please help me about this issue?( I have reduced box size, dt, C6=4 , C12=4, mass=1 and temperature. before reducing temperature is 300 and after reducing it is 2.5) -- 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] segmentation fault
I managed to run my simulation but which kind of coulomtype can I use except PME? also I get different averages for kinetic and potential energies than before reducing units I think these numbers must be the same because E*=E/epsilon (epsilon is about 0.9977) for argon. could u please help me about this issue?( I have reduced box size, dt, C6=4 , C12=4, mass=1 and temperature. before reducing temperature is 300 and after reducing it is 2.5) On Sun, Jan 16, 2011 at 12:23 AM, Mark Abraham wrote: > On 15/01/2011 8:50 PM, leila separdar wrote: > >> I have Gromacs 4.0.7 I have simulated 1000 atoms of Argon with Lenard >> Jones potential in a cubic box with linear size of 3.34. but when I reduced >> units I confront with this error >> Back Off! I just backed up md.log to ./#md.log.5# >> Reading file argon.tpr, VERSION 4.0.7 (single precision) >> >> Back Off! I just backed up argon.trr to ./#argon.trr.3# >> >> Back Off! I just backed up ener.edr to ./#ener.edr.3# >> starting mdrun 'Built with Packmol' >> 100 steps, 1000.0 ps. >> Segmentation fault >> > > What was your command line? What does the end of the logfile say? Why are > you using PME for an LJ simulation that presumably has no electrostatic > interactions? > > Mark > > > >> there is no error in energy minimization or grommp command. could u please >> help me? >> here is my md.out file iin reduced units. >> cpp = /usr/bin/cpp >> integrator = md >> dt = 0.001 >> nsteps = 100 >> nstcomm = 100 >> nstxout = 100 >> nstvout = 100 >> nstfout = 0 >> nstlog = 100 >> nstenergy = 100 >> nstlist = 10 >> ns_type = grid >> rlist = 2.9 >> coulombtype = PME >> rcoulomb= 2.9 >> rvdw= 2.9 >> fourierspacing = 0.35 >> fourier_nx = 0 >> fourier_ny = 0 >> fourier_nz = 0 >> pme_order = 4 >> ewald_rtol = 1e-5 >> optimize_fft= yes >> >> ;Berendsen temperature coupling is on in three groups >> Tcoupl = berendsen >> tau_t = 0.1 >> tc_grps= GAS >> ref_t = 2.5 >> >> ;generate velocities >> gen_vel= yes >> gen_temp= 2.5 >> gen_seed = 173529 >> > > -- > 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
[gmx-users] segmentation fault
I have Gromacs 4.0.7 I have simulated 1000 atoms of Argon with Lenard Jones potential in a cubic box with linear size of 3.34. but when I reduced units I confront with this error Back Off! I just backed up md.log to ./#md.log.5# Reading file argon.tpr, VERSION 4.0.7 (single precision) Back Off! I just backed up argon.trr to ./#argon.trr.3# Back Off! I just backed up ener.edr to ./#ener.edr.3# starting mdrun 'Built with Packmol' 100 steps, 1000.0 ps. Segmentation fault there is no error in energy minimization or grommp command. could u please help me? here is my md.out file iin reduced units. cpp = /usr/bin/cpp integrator = md dt = 0.001 nsteps = 100 nstcomm = 100 nstxout = 100 nstvout = 100 nstfout = 0 nstlog = 100 nstenergy = 100 nstlist = 10 ns_type = grid rlist = 2.9 coulombtype = PME rcoulomb= 2.9 rvdw= 2.9 fourierspacing = 0.35 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes ;Berendsen temperature coupling is on in three groups Tcoupl = berendsen tau_t = 0.1 tc_grps= GAS ref_t = 2.5 ;generate velocities gen_vel= yes gen_temp= 2.5 gen_seed = 173529 -- 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] nanoparticles
I want to simulate nanoparticles and I want to know if it is possible to simulate nanoparticles by Gromacs or not? and if yes how can I simulate a nanoparticle. thanks -- 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] Binary lennard jones
yes I have read them many times On Sun, Dec 12, 2010 at 10:41 AM, Mark Abraham wrote: > On 12/12/2010 6:08 PM, leila separdar wrote: > >> I want to simulate a binary lenard jones system. I have .top and .gro file >> for both A and B atom types . how can I mix this two atom types ? do I must >> regard the lenard jones potential between this two atom type or not? and >> where I must put C12 and C6 parameters for interaction between these two >> atoms? >> > > Have you done the necessary background reading in chapters 4 and 4 of the > manual? > > 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 > -- 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] Binary lennard jones
I want to simulate a binary lenard jones system. I have .top and .gro file for both A and B atom types . how can I mix this two atom types ? do I must regard the lenard jones potential between this two atom type or not? and where I must put C12 and C6 parameters for interaction between these two atoms? -- 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] .itp for simple atom
I am beginner with gromacs I want to simulate a system of 100 Argon atom with Lennard Jones force field but I do not know how to make .itp file I have made this lines but it made error. could anybody hep me? [ atomtypes ] ;name at.num mass charge ptypesigmaepsilon AR 1839.948 0.0A 2.54129e-011.58992e-01 [ nonbond_params ] ; ij func c6 c12 ; Encad uses strict combination rules, so no need for explicit parameters [ pairtypes ] ; ij func cs6 cs12 ; 1,4 interactions are calculated automatically, using fudge factors. ; (In the current version, the factors are 0.0, meaning no 1,4 interactions). -- 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] request
hi do I need any .pdb file for making .gro and .top file? I make .pdb file with hyperchem software and then I used pdb2gmx command in order to make .gro and .top files. but I think my way is wrong. is it true? is there anybody that done this simulation? leila On Sun, Nov 21, 2010 at 11:24 AM, Amit Choubey wrote: > Hi, > > Define an itp file which has the non-bonded info. Then define a mdp (md > parameter file) and also make a structure file (gro). Also you need a > topology file (top) which corresponds to the structure file. > > You will have to do some background work. Manual should be your friend. > > amit > > On Sat, Nov 20, 2010 at 11:32 PM, leila separdar < > separdar.le...@gmail.com> wrote: > >> I am beginner with gromacs. I would like to simulate the behavior of >> glassy materials starting with simple Lennard Jones liquid. >> please advise me as to how to begin. >> a relevent flowchart or tutorial would be of immerse help >> thank you very much indeed. >> >> -- >> 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 > -- 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] request
I am beginner with gromacs. I would like to simulate the behavior of glassy materials starting with simple Lennard Jones liquid. please advise me as to how to begin. a relevent flowchart or tutorial would be of immerse help thank you very much indeed. -- 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
