On Nov 29, 2010, at 5:58 PM, sreelakshmi ramesh wrote: > Basically i have been using a sampling method called FFS to calculate the > rate constant for folding of a protein .The umbrella sampling done on the > system shows there is high barrier between the reac an prod states The phase > spece regions in ffs method are divided in to many non -intersecting > interfaces along the reaction coordinate.i have started the simulation from > reactant region and ended up at a point in between the reactant and product > state The transition state is not attained so far.The simulation is stopped > between the transition state and reactant .I have 100 such configuration > stored at that state.Now i have to select every config at that state at > random amd it should start with the same velocity when it was stored at that > state and continue the simulation to reach the next state.so i am reading the > position and velocities of the con-fig from previously saved trajectory of > that con-fig.so since randomly if the same con fig s selected twice the > trajectory is the same which i don't want.
I assume the FFS you refer to is Forward Flux Sampling. I don't think you can use this method for fully deterministic dynamics, for precisely the reason you describe. You have to introduce some form of stochasticity, but I am not sure if random changes in the velocities at the interface configurations are the best way to do that. You might want to take a look at section 3.2 of http://dx.doi.org/10.1088/0953-8984/21/46/463102 There are, however, legitimate uses of changing the velocities of a configuration that are not complete reassignment from a Maxwell distribution. In Transition Path Sampling, for example, you need to create a trajectory that is "close" to another one for a while, and you usually do that by making a "small" change to a configuration's velocity. The details of how you make this change enter in the acceptance probability of a TPS trial move. I don't think Gromacs provides this functionality out of the box, so you probably have to write your own code to do that. Hope this helps, Lutz -- 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
