Dear Moeed: > I tried to get the same results as you got for density and total energy > starting from the 8 chains is the box. I used the revised mdp file and since > PME option takes much time I used shift instead for a moment to verify if I > can get the density you obtained. Also I used constraints for bonds. density > I get after 1800ps is 850 kg/m3 while what you got is a slightly different > (after 1000ps density varies around 880!). Also the total energy you have is > bout 2300 whereas I get somethong around 12000!. I dont know why they are so > different..
Different methods for electrostatics give very different absolute energies as a result. C'est la vie... > In the second trial I used "constraints = none" just the "shift" > for electrostatics is not the same as the mdp file you suggested. again > results are not the same for total energy (20000 Kj/mol). Below is the > average values...also simulation crashes at 1550 ps and the last density I > am getting is 834! still less than what you got. dont really know why > results are not the same. Because the methods are not identical. Please read about electrostatics treatment to understand this issue. >The reason simulation crashes could be due to > dt=0.002 while removing constraints? It can be due to C-H fast oscillations, for example. Maybe it is a good idea to try SHAKE for these bonds if the time-step is so critical for you. > 1- What I see is that the system is getting compressed to a size of around 3 > 3 3 nm is the first 20ps abruptly and in the remainder of time system > reaches equilibrium... This is very different approach than what I was > trying doing before. I used berendsen scheme for pressure coupling and box > reduced is size slowly but I had difficulty reaching the size I want and > most of the simulations crashed. Does this mean berenden is not suitable for > compressing system for all systems? I did not ever observe that. Please also note that I used semiisotropic pressure coupling for your system because of its specific [rather anisotropic] structure with long molecules. I suppose this option should provide more realistic density in your particular case. > 2- You said I dont need NVT at all. But if I want to study the system I get > from NPT giving the density I want, can I not do NVT for a fixed system size > and calcualte energies or other quantities I am after? Of course, you can. This is the only way to have a constant density. Good luck. Vitaly -- gmx-users mailing list gmx-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