Re: [gmx-users] (no subject)
Could you paste your .top file and the command your add ions? Maybe the Cl- ion was also added when you added Na+ ion? On Tue, Jun 12, 2012 at 1:18 PM, tarak karmakar tarak20...@gmail.comwrote: Dear All , I am facing problem in matching the coordinates number in this two files, em.gro and toplogy.top. I have tried with changing the number of solvents, adding ions (Na+) but in vain *Note :: My system has ' -1.00 ' charge ...so I have added one Sodium ion* So can anyone please get me out of this trouble ??? Fatal error: number of coordinates in coordinate file (em.gro, 64506) does not match topology (toplogy.top, 64504) -- *Tarak Karmakar Molecular Simulation Lab. Chemistry and Physics of Materials Unit Jawaharlal Nehru Centre for Advanced Scientific Research Jakkur P. O. Bangalore - 560 064 Karnataka, INDIA Ph. (lab) : +91-80-22082809 * -- 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
Re: [gmx-users] How to prevent box shrinking incessantly at x and y when doing membrane simulation using semiisotropic couple type?
Dear Chris Thanks again for your reply. On Sat, Jun 2, 2012 at 10:52 PM, Christopher Neale chris.ne...@mail.utoronto.ca wrote: I suspect that you can find an equation to relate the surface tension to the ratio of the pressure along z to the pressure along xy that is required to maintain the unit cell of a semi-isotropic simulation approximately constant when you use the same compressibility in all dimensions. Actually there is an equation to calculate surface tension by lateral pressure and normal pressure. [image: Inline image 1] 1/2 shows there are two interfaces. Lz is the lenth of box-z. Pn(Z) is normal pressure. Pt(Z) is (press-x + press-y)/2. But pressure must be gotten by correct simulation. You might even find an equation that was based on the rate of unit cell deformation when applying the same pressure in all dimensions. Since this is a non-equilibrium simulation you may need to run many of them to get an average rate. Sorry I don't know how to contact the rate to the surface tension. Or should I use this rate to set my pressure or compressbility? Alternatively, you might consider simulating a spherical glob of decane in a water bath and finding equations that relate the aspherocity to the surface tension. It's interesting and I am thinking about it. It needs a lot of work to do. aha If I were you, I'd look into physics textbooks to find some relation like this that you can use. Chris. -- 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 image.png-- 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 prevent box shrinking incessantly at x and y when doing membrane simulation using semiisotropic couple type?
Sorry for my carelessness. Before nose-hoover, Parrinello-Rahman, I have done v-rescale, berendsen already. tau_t = 0.1, tau_p = 0.5. Hugh. On Sat, Jun 2, 2012 at 12:43 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 2/06/2012 1:11 PM, Klniu wrote: Dear Gromacs users, I am doing a membrane simulation. The system are two layers composed by surfactants. other molecule are decane and water. The system like this: decane --- surfactant --- water --- surfactant --- decane My research is to get the surface tension between decane and water. I mainly use NPT simulation to reach equilibrium and product. when I set pcoupl = semiisotropic and compressibility = 4.5e-5 4.5e-5, the box at x and y will shrink incessantly and then the system crashes. My question is: 1. Is my direction of work worng? There is another way to do this simution? 2. how can I get surface tension? Equilibration with P-R pressure coupling is asking for trouble. Use Berendsen to get close, then switch. Otherwise, see http://www.gromacs.org/Documentation/Terminology/Blowing_Up Mark The content of mdp file is below: ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 10 ; ns algorithm (simple or grid) ns_type = grid ; Periodic boundary conditions: xyz, no, xy pbc = xyz periodic_molecules = no ; nblist cut-off rlist= 1.0 ; long-range cut-off for switched potentials rlistlong= -1 ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = PME rcoulomb-switch = 0 rcoulomb = 1.0 ; Relative dielectric constant for the medium and the reaction field epsilon_r= 1 epsilon_rf = 1 ; Method for doing Van der Waals vdw-type = Cut-off ; cut-off lengths rvdw-switch = 0 rvdw = 1.4 ; Apply long range dispersion corrections for Energy and Pressure dispcorr = EnerPres ; Extension of the potential lookup tables beyond the cut-off table-extension = 1 ; Seperate tables between energy group pairs energygrp_table = ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.135 ; FFT grid size, when a value is 0 fourierspacing will be used fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ; EWALD/PME/PPPM parameters pme_order= 4 ewald_rtol = 1e-05 ewald_geometry = 3d epsilon_surface = 0 optimize_fft = yes ; IMPLICIT SOLVENT ALGORITHM implicit_solvent = No ; GENERALIZED BORN ELECTROSTATICS ; Algorithm for calculating Born radii gb_algorithm = Still ; Frequency of calculating the Born radii inside rlist nstgbradii = 1 ; Cutoff for Born radii calculation; the contribution from atoms ; between rlist and rgbradii is updated every nstlist steps rgbradii = 1 ; Dielectric coefficient of the implicit solvent gb_epsilon_solvent = 80 ; Salt concentration in M for Generalized Born models gb_saltconc = 0 ; Scaling factors used in the OBC GB model. Default values are OBC(II) gb_obc_alpha = 1 gb_obc_beta = 0.8 gb_obc_gamma = 4.85 gb_dielectric_offset = 0.009 sa_algorithm = Ace-approximation ; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA ; The value -1 will set default value for Still/HCT/OBC GB-models. sa_surface_tension = -1 ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling tcoupl = Nose-Hoover nsttcouple = -1 nh-chain-length = 10 ; Groups to couple separately tc-grps = OIL DRG SOL ; Time constant (ps) and reference temperature (K) tau_t= 0.5 0.5 0.5 ref_t= 300 300 300 ; Pressure coupling pcoupl = Parrinello-Rahman pcoupltype = semiisotropic nstpcouple = -1 ; Time constant (ps), compressibility (1/bar) and reference P (bar) tau_p= 2.0 2.0 compressibility = 4.5e-5 4.5e-5 ref_p= 1.0 1.0 I have post a mail in list but my description is not clear. http://lists.gromacs.org/pipermail/gmx-users/2012-June/072000.html Thank you. Hugh. -- 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
[gmx-users] What is the right way to get reasonable interfacial tension of surfactant at oil/water interface
Dear Gromacs users, I have do simulation of surfactant at oil/water interface for a long time. But I find it too difficult to get a reasonable interfacial tension. The key question is the pcoupltype. My system: Box size: 3.0 * 3.0 * 13 Molecule Number: decane 230, water 2041 pcoupltype = semiisotropic Gromacs version: 4.5.5 1. When I set compressibility = 4.5e-5 4.5e-5. Surfactant number is 32 . The box will be shrink at x and y. At last simualion will end for a fatal error: One of the box vectors has become shorter than twice the cut-off length or box_yy-|box_zy| or box_zz has become smaller than the cut-off. For more information and tips for troubleshooting, please check the GROMACS. 2. When I add the number of surfactants to 40. compressibility = 4.5e-5 4.5e-5. The interfacial tension is -20bar/nm for two interfaces. It is not reasonable because it should be positive. 3. When I compressibility = 0 4.5e-5. Surfactant number is 32. The interfacial tension is 794bar/nm for two interfaces. My question is: What is the right way to simulate for this system? My work confused me too much. Very appreciate for you help. Hugh -- 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 is the right way to get reasonable interfacial tension of surfactant at oil/water interface
Dear Chris: Thank you for your help. Maybe I can try it as this. First set x and y fixed by setting compressibility = 0 4.5e-0.5 until the system reaching equilibrium and then release. If it sounds reasonable. I am trying to do it. Dear Hugh: I can't answer your question, but I can address the error message that you see. Basically, your semi-isotropic pressure coupling allows the surface area of the water-decane interface to get smaller as z increases and x and y decrease. In a system with only water and decane, this will continue until you have a single file of decane aligned in z. To avoid this, you need to use semi-isotropic pressure coupling but set the compressibility to zero in the z dimension (or, alternatively set the compressibility to zero in both x and y). This will get rid of the error message, as I see that you have already noted. So I guess that all I can tell you is that your first option is not going to be possible and that your second option is giving you the wrong value because your surfactants are fighting the elongation of your box along z, but the effect persists. Chris. -- original message -- Dear Gromacs users, I have do simulation of surfactant at oil/water interface for a long time. But I find it too difficult to get a reasonable interfacial tension. The key question is the pcoupltype. My system: Box size: 3.0 * 3.0 * 13 * Molecule Number: decane 230, water 2041* * pcoupltype = semiisotropic* Gromacs version: 4.5.5 1. When I set compressibility = 4.5e-5 4.5e-5. Surfactant number is 32 . The box will be shrink at x and y. At last simualion will end for a fatal error: One of the box vectors has become shorter than twice the cut-off length or box_yy-|box_zy| or box_zz has become smaller than the cut-off. For more information and tips for troubleshooting, please check the GROMACS. 2. When I add the number of surfactants to 40. compressibility = 4.5e-5 4.5e-5. The interfacial tension is -20bar/nm for two interfaces. It is not reasonable because it should be positive. 3. When I compressibility = 0 4.5e-5. Surfactant number is 32. The interfacial tension is 794bar/nm for two interfaces. My question is: What is the right way to simulate for this system? My work confused me too much. Very appreciate for you help. Hugh -- 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] What is the right way to get reasonable interfacial tension of surfactant at oil/water interface
Very thank you for your suggestion and being so kind. I will write a new detailed subject and explain my purpose. On Sat, Jun 2, 2012 at 10:23 AM, Christopher Neale chris.ne...@mail.utoronto.ca wrote: No, the point is that the equilibrium surface area is near zero in the context of PBC and you need special tricks to keep the system away from that equilibrium. There will always be a force toward reducing the surface area of the hydrophobic/hydrophilic interface. It is possible to disallow this force to cause system relaxation by using an incompressible Cartesian z (or x and y), but as soon as you let that go the system will then relax toward the tall and thin column of aliphatic chains. Perhaps you should return to the list with a detailed description of what you are trying to accomplish and you might get some help. I doubt that I can help that part, but there is likely somebody out there who can. Also, you will increase your chances of getting help from somebody like me (expert gromacs user who is totally ignorant of your particular field of study) by giving proper explanations of thing like the interfacial tension of surfactant at oil/water interface. I know that it makes sense to you (and probably lots of other people), but I for one don't know exactly what you are trying to accomplish. Chris. -- original message -- Dear Chris: Thank you for your help. Maybe I can try it as this. First set x and y fixed by setting compressibility = 0 4.5e-0.5 until the system reaching equilibrium and then release. If it sounds reasonable. I am trying to do it. Dear Hugh: -- 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
