[gmx-users] Question about the Marrink's CG model
Dear GMXers: I'm sorry to disturb you. I have a question about the Marrink's coarse-grained model, Marrink, et al. Coarse Grained Model for Semiquantitative Lipid Simulations. J. Phys. Chem. B 2004, 108, 750-760. In the Marrink's CG model, the electrostatic Coulombic potential is computed via cutoff scheme. In the original paper, the cutoff method is employed with relative dielectric constant \epsilon=20 for explicit screening. Does it mean the parameter of force field is only customized for the cutoff method? As known that the Ewald method is better than the cutoff scheme for the long-range electrostatic interaction. I want to know whether the Ewald method is also OK for this model? How can I test it? I have simulated a similar system via two method respectively, which includes a big charged nano-scale particle (~6nm). But I find that the results of cutoff scheme are quite different from the PME's results. I don't know which one is right. Another question is how to get the relative dielectric constant for a CG model. I'm not familiar with this topic, but I think it is the key of the above question perhaps. Yet, there are not some details in the original paper. In some other paper about different CG models, I don't find some information about this topic. Could someone please give me some refs about the computational details? Thank you very much. Li Yang ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] how to compute bending modulus of the membrane with NPs
Dear all I'm trying to measure the bending modulus (Kc) of lipid bilayer. I've found some papers, showing that spectral intensity needs to be calculated using the wave vector q. This method has been applied directly for pure membrane, or for bilayers with cholesterol. In my simulations, there is a colloid particle immerses into the inner or adsorbs on the surface of the lipid bilayer. I want to compute how the interaction of particles to affect the bending modulus of the membrane. But I'm not sure whether this method can be applied directly in above cases? If not, how can I get it? What about the spontaneous curvature? Thank you very much. Any suggestion or reference will be appreciated! Li Yang ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: RE: [gmx-users] how to set pull code in gmx 4
Hi Berk Thanks for your reply If you use pull_geometry=distance you need to set the reference distance, which would be (assuming you want 1 nm): pull_init1 = 1 Sorry for my poor expression. Take a example, In gmx 3.3, the pull dimension and position can be writen as: pull_type = umbrella ; umbrella sampling pull_dim = N N Y ; pulling performed in Z dimension pos1 = 0 0 1 ; the reference distance in Z dimension is 1nm In gmx 4, for pull_init1 = 1, which dimension of the reference distance does it mean ？ Or say, there is still a single pulling performed in one dimension, like gmx 3.3, and when setting pull_dim = N N Y, the pull init1=1 means the reference distance in Z dimension is 1nm; while pull_dim=Y N N means the reference distance in X dimension is 1nm？ Maybe my thinking sounds stupid, I don't know. Waiting for your reply. Li Yang ___ 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 set pull code in gmx 4
Dear all I cannot understand the explanations about settings of pull code in the gmx 4. Take a example, there are two particles in the system, and I want to reproduce the LJ potential using umbrella sampling. The settings in gmx 3.3.3 is following: = .. runtype = umbrella ngroups = 1 group_1 = Arg2 reference_group = Arg1 .. pulldim = N N Y K1 = 700 POS1 = 0 0 1 == But I don't know how to set it in gmx 4 Following is the settings in gmx 4: == ; COM PULLING ; Pull type: no, umbrella, constraint or constant_force pull = umbrella ; --- runtype in gmx 3.3.3 ; Pull geometry: distance, direction, cylinder or position pull_geometry = distance ; Select components for the pull vector. default: Y Y Y pull_dim = N N Y ; --- pulldim in gmx 3.3.3 ; Cylinder radius for dynamic reaction force groups (nm) pull_r1 = 1 ; Switch from r1 to r0 in case of dynamic reaction force pull_r0 = 1.5 pull_constr_tol = 1e-06 pull_start = no pull_nstxout = 10 pull_nstfout = 1 ; Number of pull groups pull_ngroups = 1 ; --- ngroups in gmx 3.3.3 ; Group name, weight (default all 1), vector, init, rate (nm/ps), kJ/(mol*nm^2) pull_group0 = Arg2 ; --- reference_group in gmx 3.3.3 pull_weights0 = pull_pbcatom0 = 0 pull_group1 = Arg1 ; --- group1 in gmx 3.3.3 pull_weights1 = pull_pbcatom1 = 0 pull_vec1 = 0.0 0.0 0.0 pull_init1 = 0.0 pull_rate1 = 0 pull_k1 = 700 ; --- k1 in gmx 3.3.3 pull_kB1 = 0 == if right, which parameter corresponds with pos1 in gmx3.3.3? I must apologize in advance if I miss some details in the manual. Thank you very much Li Yang ___ 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: gmx-users Digest, Vol 53, Issue 90
Hi Ran Thank you for your reply. I'm sorry that I miss the message. (1) 6 eigenvalues represent rotation and translation. For (very) small molecules, these can be quite substantial, see Carlsson and Aqvist, /J. Phys. Chem. B,/ *109* (13), 6448 -6456, 2005. By fitting you remove the rotation and translation. You can search the literature for papers that discuss the QH approximation as well. The motions are not really harmonic - this is why it's an approximation. I've received very similar results to Carlsson and Aqvist for benzene and palmatic acid with GMX. (2) The values you get depend on the sampling and the conversion of the simulations. To improve sampling, you have to store the coordinates frequently enough (so you get more samples). In addition, the simulation should be long enough to give you meaningful results - and both depend on the system which you study. Checking for convergence can be done by repeating the calculations on different time windows, as you suggested. Sorry, I don't quite catch your mind. How to get the convergence variation of the entropy? Whether or not the time split method is right? eg, time points: 0, 1, 2, 3, 4, 5. and time stage：0-1, 0-2, 0-3, 0-4, 0-5, right? why not 0-1, 1-2, 2-3, 3-4, 4-5. In the maillist of gmx, the latter is not wrong because of undersampling, I don't know this meaning. Could you please offer me some suggestions or refs? The method of covariance matrix QH can estimate the up-limit of entropy, how to know the error band ? Thank you very much. (3) In entropy calculations, a system need to run a long time for entropy convergence, the time seems to be longer than the one which needed for energy convergence. While, for equilibrium thermodynamics simulations, how to justify whether or not the system has achieving a equilibrium stage, based on energy convergence or entropy confvergence? (4) For the example mentioned in the paper Ioan Andricioaei_JChemPhys2001_115_6289. I use your perl script for entropy calculation. But I don't reproduce the result. The needed time of entropy convergence is longer than the time mentioned in the paper, and so larger of my entropy. I don't know why, perphas the simulation conditions is not right. My simulation files are included in the attachment. Could you give some suggestions? BTW, in line 77 of your script: $w=$ev*$u*10**(-18), Does 10^-18 mean nm^-2? ___ 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 measure the surface tension of membrane by inclusion
Hi I have some questions about the surface tension calculations: 1. For the formula, \gamma_m=(P_N - P_L) * L_z / 2, is it only available for a flat surface, like a lipid bilayer in water ? For example, the surface fluctuation of lipid bilayer often occur in the simulation, sometimes, the surface is not flat but bending, in such a case, is the formula still available? What about the vesicle? 2. In my system, there are a bilayer patch and a NP of ~10nm, they are all in water. At the beginning (state 1), NP and the bilayer don't contact each other. After some nanoseconds runtime, NP adsorbs on the surface of the bilayer (state 2). Finally(state 3), the NP embeds into the inner of the lipid bilayer. In this case, how can I measure the changing surface tension during the simulation? Is the formula above available for my system? In state 1, is that meaning there are four interface in the system? What about the case (state 2,3) that the NP contacting the bilayer ? I hope I've describe my questions clearly. Any suggestion or recommended reference will be appreciated. Thank you very much. Sincerely Li Yang [EMAIL PROTECTED] 2008-07-17 ___ 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
