---------- Forwarded message ---------- From: Apramita Chand <apramita.ch...@gmail.com> Date: Fri, Aug 26, 2016 at 6:56 PM Subject: Regarding correct way to calculate diffusion constant To: gmx-us...@gromacs.org
Dear All, I want to calculate the diffusion constant of urea in my system. I used g_msd for this purpose and the value came to be 8.279e -08 (+/-8.85e-09) 1e -5 cm^2/s. Since the value is quite low, I wanted it to check it with result from VACF. Any explanations as to why g_msd yielded a low value for a system conatining 5 urea,751 water and a single protein molecule? I ran the calculations again using 17 urea,791 water and protein. The value comes out to be negative with the same exponent as mentioned above for urea diffusion. The water diffusion values seem to be normal . I generated the movie for the trajectory and urea certainly has movement though the molecules never wander much from their positions. In addition,the radial distribution functions generated for protein-urea shows site-site interactions but the tail of the g(r) stops short at around 3 A and does not extend to the bulk(higher distances). What could be wrong in the simulation? I'm using GROMACS 4.5.7 and GROMOS 53a6 parameters. PLease help Thanking you, yours sincerely, Apramita Chand -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
