[gmx-users] changing the velocity in trajectory file

sreelakshmi ramesh sree.lakshmi at research.iiit.ac.in
Tue Nov 30 05:52:41 CET 2010

Lutz ya you are true but as you said how can i change the velocity  for a
config every move as in TPS?since i have not done tps i have no idea abt


On Tue, Nov 30, 2010 at 9:15 AM, Lutz Maibaum <lutz.maibaum at gmail.com>wrote:

> 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
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