<div dir="ltr">Dear Xavier,<br><br>I am sorry for posting an email which is not directly related to the gromacs. <br><br>I have created a trajectory which contains the time dependent orientational changes of my reference structure (from the original trajectory generated by gromacs). I obtained the average rotational correaltion function of a few selected vectors from the newly generated trajectory. From these I wanted to obtain the average correlation times by fitting the generated correlation function to a function. <br>
<br>I have looked at the literature aswellas a couple of recently published papers (JCTC, 2006, 2, 1228), the total correlation function is separated as follows:<br><br>C(total) = C(rot) * C(int)<br><br>here, C(rot) can be fitted to 1/5 * exp (-t/t_c); where "t_c" is the correlation time. <br>
<br>My question is:<br><br>If I use this function, when t=0, the function will have a value of 0.2 and how can I use this function to fit the rotational correaltion function (where, I have a decay starting from 1 when t=0). If I dont use the 1/5 scaling factor, the fit is good and I obtained the correlation time as 0.96 ns. ( I really dont have any idea whether it is low or high).<br>
<br>I also wanted to know, after a couple of nano seconds, the correlation function becomes -ve. What these -ve correlations mean ?<br><br>Thanks and Regards,<br>Ram.<br></div>