[gmx-users] Negative pressure
Dear user, What is the physical significance of negative average pressure in NVT MD simulations? Thank you. -- 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] Optimal number of time origins in the calculation of block-averaged time correlation functions
Dear users, I am comparing different schemes for computing the self-diffusion of a system. One of the approches I am considering is using block averages. I have a 50 ns long trajectory and I want to compute the block-averaged diffusion constant as follows: (1) Divide the trajectory into blocks of 2 ns (25 blocks of equal length) (2) For each block compute the rmsd over all particles and Nt time origins (25 diffusion constants in all) (3) Compute the average and standard deviation of the 25 diffusion constants Point (2) above is where things get tricky. When you read previous works, authors are usually not specific about the exact values of the parameters they used. Currently I choose the number of origins (Nt) and the correlation time (Tc) arbitrarily. It is obvious that the maximum value of Nt is BL/2, where BL is the length of each block and the maximum value of Tc = delta_t * BL/2. My question is how to determine the optimal number of time origins Nt and Tc per block. Suggestions from experienced users or any reference to an article which discusses a scheme for choosing the Nt and Tc would be much appreciated. I am a novice so kindly be as specific as possible in your response. Thank you very much -- 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] Stabilizing a heavy metal ion in solution
Dear users, I would like to know if users can give me a couple of suggestions on how to control large temperature swings of a heavy metal ion like Uranium in solution. The temperature of the metal ion fluctuates considerably and hardly stabilizes--even in the long time limit while the solvent temperature stabilizes easily. The gromacs 'what not to do" list strongly discourages against coupling the ion and solvent to separate thermostats. I would like to know if experienced users can give tips on how to alleviate this problem. -- 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] SPC/E water RDF
Dear users, Since I'm new to MD, I coded SPC/E water in the NVT emsemble. Basic ingredients: (1) Number of water molecules N=216 (2) Mass of O = 16 Mass of H = 1 (3) Box density (Periodic Boundary Condition) is exactly 1g/cc (L =18.6205 Angstrom) (4) SPC/E LJ parameters from Berendsen's original 1987 paper (5) Coulomb interaction: Ewald sum Real space ewald: Minimum image convention Ewald convergence parameter for reciprocal sum = 5/L (L is the box length in Ang) Fourier cut-off for ewald reciprocal sum |G| =2*pi*|n|/L, where |n| < 27 (6) Nose-Hoover chain NVT (single chain, single thermostat per chain) (7) Time step 1 fs, velocity verlet solver, RATTLE was used to constrain bond lengths and angle, and correct velocities. (8) 100 ps equlibration, 400 ps production (configuration was saved every 25 fs) Everything is fine (energies are stable, etc.) except the second peak in the O-O rdf. The first peak is fine but my second peak seems flat. I find this troubling since all the rdfs I've seen in literature as well the experimental plot have a well-defined second peak. I must mention that in all the papers I've seen the ensemble is NPT (I've not seen NVT yet). In any case, I was expecting my result to match previously published results closely. Can anyone point out what I am doing wrong?? Is NVT not a good ensemble for water simulation?? I'll appreciate it if someone can refer me to a paper that discusses this. -- 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] SPC/E water rdf
Dear users, Since I'm new to MD, I coded SPC/E water in the NVT emsemble. Basic ingredients: (1) Number of water molecules N=216 (2) Mass of O = 16 Mass of H = 1 (3) Box density (Periodic Boundary Condition) is exactly 1g/cc (L = (4) SPC/E LJ parameters from Berendsen's original 1987 paper (5) Coulomb interaction: Ewald sum Real space ewald: Minimum image convention Ewald convergence parameter for reciprocal sum = 5/L (L is the box length in Ang) Fourier cut-off for ewald reciprocal sum |G| =2*pi*|n|/L, where |n| < 27 (6) Nose-Hoover chain NVT (single chain, single thermostat per chain) (7) Time step 1 fs, velocity verlet solver, RATTLE was used to constrain bond lengths and angle, and correct velocities. (8) 100 ps equlibration, 400 ps production (configuration was saved every 25 fs) Everything is fine (energies are stable, etc.) except the second peak in the O-O rdf. The first peak is fine but my second peak seems flat. I find this troubling since all the rdfs I've seen in literature as well the experimental plot have a well-defined second peak. I must mention that in all the papers I've seen the ensemble is NPT (I've not seen NVT yet). In any case, I was expecting my result to match previously published results closely. Can anyone point out what I am doing wrong?? Is NVT not a good ensemble for water simulation?? I'll appreciate it if someone can refer me to a paper that discusses this. -- 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] maximum cut-off in Minimum image convention
Dear users, I wish to ask a question regarding the maximum cut-off in the minimum image convention (MIC). According to my understanding, MIC ensures that the separation between two particles i and j along each coordinate axes, namely, xi- xj, yi-yj, and zi-zj, is in the interval (-0.5L, 0.5L), where L is the box length (assumed the box to be cubic). This implies that distance rij can vary between 0 and 0.5L*sqrt(3). In order words the maximum separation should be less than half the diagonal: for example if i is located at (0,0,0) and j is located at the corner (0.49L, 0.49L, 0.49L). However, I read a couple of text books and online notes that claim that if r > 0.5L, then MIC is violated. Specifically, this means that 0.5L < rij < 0.5L*sqrt(3) violates MIC. I find this confusing. I have been grinding hard to understand this point but I just cannot figure it out. In short my claim is that in MIC, rij can be at most half the diagonal length whereas the textbook says that rij can be at most half the box length. If I am wrong, can someone explain the flaw in my argument? 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/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
