On Wed, Dec 19, 2012 at 11:27 PM, Ahmet yıldırım <[email protected]>wrote:
> Dear users, > > When analyzing some of the simulations; > I get 312 K, 310 K or 308 K instead of 300K (the t_ref value for the whole > system). > 1. What is the reason for the increase of temperature? For example it can > be cutoff artifacts. What else can be? > Any kind of integration inaccuracy could lead to heating, e.g. too large a time step. The time period after equilibration over which you observed the average temperature, and the size of the system is a necessary part of reporting a temperature, else it's meaningless. Too little time or an average over too few atoms leads to large fluctuations and thus low expectations that the average of the sample will be correct. 2. To get the the error small tau_t can be reduced. What is the minimum > value for tau_t? > That's probably treating the symptoms, not the disease. Sometimes, the pressure in the output files is high ( 7 bar, 6 bar or 1.5 > bar instead of 1 bar). > I.The reason for this? > II. tau_p can be reduced as temperature. And what is the minimum value for > tau_p? > See GROMACS webpage on pressure coupling and measuring pressure. Manual discussion also. Briefly, what could be the reasons for the increase in temperature or > pressure? What are your suggestions for the solution? > Follow protocols in publications that discussed how and why they chose their settings for the force field of interest, or which demonstrated their choices were good. Making things up, or copying others blindly is a recipe for wasting computer time. Mark -- gmx-users mailing list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
