diff --git a/user-doc/figs/belfast-6-phialone.pdf b/user-doc/figs/belfast-6-phialone.pdf deleted file mode 100644 index 555580dd3fef7e58755dec5e31c6eae71c0433ba..0000000000000000000000000000000000000000 Binary files a/user-doc/figs/belfast-6-phialone.pdf and /dev/null differ diff --git a/user-doc/figs/belfast-6-phialone.png b/user-doc/figs/belfast-6-phialone.png new file mode 100644 index 0000000000000000000000000000000000000000..a7214945078c87d92628caac8bb3fef3fa1f3c16 Binary files /dev/null and b/user-doc/figs/belfast-6-phialone.png differ diff --git a/user-doc/figs/belfast-6-wtb15.pdf b/user-doc/figs/belfast-6-wtb15.pdf deleted file mode 100644 index 5b7e089a447e16fed5073458ffa2e534a4f8a7e3..0000000000000000000000000000000000000000 Binary files a/user-doc/figs/belfast-6-wtb15.pdf and /dev/null differ diff --git a/user-doc/figs/belfast-6-wtb15.png b/user-doc/figs/belfast-6-wtb15.png new file mode 100644 index 0000000000000000000000000000000000000000..b1fdd8dda82934765aaf4a595ad5de90fc95a97e Binary files /dev/null and b/user-doc/figs/belfast-6-wtb15.png differ diff --git a/user-doc/figs/belfast-6-wtb6.pdf b/user-doc/figs/belfast-6-wtb6.pdf deleted file mode 100644 index 1601d6aa86fb7a48e09ab93f1c8c18186ff0705b..0000000000000000000000000000000000000000 Binary files a/user-doc/figs/belfast-6-wtb6.pdf and /dev/null differ diff --git a/user-doc/figs/belfast-6-wtb6.png b/user-doc/figs/belfast-6-wtb6.png new file mode 100644 index 0000000000000000000000000000000000000000..91c218fda69694229443ce8137cfbc349b1f6b64 Binary files /dev/null and b/user-doc/figs/belfast-6-wtb6.png differ diff --git a/user-doc/figs/belfast-7-ptmetadh.pdf b/user-doc/figs/belfast-7-ptmetadh.pdf deleted file mode 100644 index 1bab5709d3e739350f590a9f7353dc0e2a655291..0000000000000000000000000000000000000000 Binary files a/user-doc/figs/belfast-7-ptmetadh.pdf and /dev/null differ diff --git a/user-doc/figs/belfast-7-ptmetadh.png b/user-doc/figs/belfast-7-ptmetadh.png new file mode 100644 index 0000000000000000000000000000000000000000..85362ae91801928fa2b2bf72302282686c9d31e8 Binary files /dev/null and b/user-doc/figs/belfast-7-ptmetadh.png differ diff --git a/user-doc/figs/belfast-7-ptmetadhidd.pdf b/user-doc/figs/belfast-7-ptmetadhidd.pdf deleted file mode 100644 index 49aac7c2cec91c29df12420b942663f8647d88fe..0000000000000000000000000000000000000000 Binary files a/user-doc/figs/belfast-7-ptmetadhidd.pdf and /dev/null differ diff --git a/user-doc/figs/belfast-7-ptmetadhidd.png b/user-doc/figs/belfast-7-ptmetadhidd.png new file mode 100644 index 0000000000000000000000000000000000000000..57156d3dcef5dbce09b7a7432f273255330986f6 Binary files /dev/null and b/user-doc/figs/belfast-7-ptmetadhidd.png differ diff --git a/user-doc/tutorials/belfast-6.txt b/user-doc/tutorials/belfast-6.txt index 7bafef618c4d8336a51a55dfbca5690cbb80d907..4ab89bab7ad1bf4a42a0457020184628061a3bfb 100644 --- a/user-doc/tutorials/belfast-6.txt +++ b/user-doc/tutorials/belfast-6.txt @@ -375,7 +375,7 @@ without further rescaling needed. We can plot the time evolution of the CVs along with the height of the Gaussian. \anchor belfast-6-wtb6-fig -\image html belfast-6-wtb6.pdf "Time evolution of the CVs and Gaussian height during the first 2.5 ns of a well-tempered metadynamics simulation with biasfactor equal to 6." +\image html belfast-6-wtb6.png "Time evolution of the CVs and Gaussian height during the first 2.5 ns of a well-tempered metadynamics simulation with biasfactor equal to 6." The system is initialized in one of the local minimum where it starts accumulating bias. As the simulation progresses and the bias added grows, the Gaussian height is progressively reduced. @@ -391,7 +391,7 @@ this biasfactor is not large enough to allow for the system to escape from the i in the time scale of this simulation. \anchor belfast-6-wtb15-fig -\image html belfast-6-wtb15.pdf "Time evolution of the CVs and Gaussian height in a 5 ns long well-tempered metadynamics simulation with biasfactor equal to 1.5." +\image html belfast-6-wtb15.png "Time evolution of the CVs and Gaussian height in a 5 ns long well-tempered metadynamics simulation with biasfactor equal to 1.5." Following the procedure described for standard metadynamics in the previous example, we can estimate the free energy as a function of time and monitor the convergence of the @@ -435,7 +435,7 @@ Let's look at the HILLS file, in particular at the time serie of the CV psi and Gaussian height. \anchor belfast-6-phialone-fig -\image html belfast-6-phialone.pdf "Time evolution of psi and Gaussian height in a well-tempered metadynamics simulation using psi alone as CV." +\image html belfast-6-phialone.png "Time evolution of psi and Gaussian height in a well-tempered metadynamics simulation using psi alone as CV." From this plot, we observe a nice diffusive behavior of the CV psi when the Gaussian height is already quite small. This happens until t=3 ns, when the CV seems to be stuck for a while in a small region diff --git a/user-doc/tutorials/belfast-7.txt b/user-doc/tutorials/belfast-7.txt index f84df743a6b80e69ca20f2e2a9e0c353b96b93b1..b3c24ae72c89c6b494f81758f444023d66cbe10f 100644 --- a/user-doc/tutorials/belfast-7.txt +++ b/user-doc/tutorials/belfast-7.txt @@ -328,7 +328,7 @@ without the use of PT (see \ref belfast-6-exercise-5), here we can focus on the the PTMetaD simulation. Let's compare the behavior of the biased variable psi in the two simulations: \anchor belfast-7-ptmetadh-fig -\image html belfast-7-ptmetadh.pdf "Time serie of the biased CV psi in a well-tempered metadynamics and PTMetaD simulations." +\image html belfast-7-ptmetadh.png "Time serie of the biased CV psi in a well-tempered metadynamics and PTMetaD simulations." In well-tempered metadynamics (left panel), the biased variable psi looked stuck early in the simulation (t=3 ns). The reason was the transition of the other hidden degree of freedom phi from one free-energy basin @@ -336,7 +336,7 @@ to the other. In the PTMetaD case (right panel), this seems not to happen. To be we can plot the time evolution of the hidden degree of freedom phi in the two cases. \anchor belfast-7-ptmetadhidd-fig -\image html belfast-7-ptmetadhidd.pdf "Time serie of the CV phi in a well-tempered metadynamics and PTMetaD simulations." +\image html belfast-7-ptmetadhidd.png "Time serie of the CV phi in a well-tempered metadynamics and PTMetaD simulations." Thanks to the excursions at high temperature, in the PTMetaD simulation the transition of the CV phi between the two basins is accelerate. As a result, the convergence of the reconstructed free energy in psi