metadynamics

[isaac gimenez]

Dear all,

I am starting to run metadynamics in a crown ether system with strontium and chlorides.

the idea is to run metadyanimcs with 2 collective variables, in order to understand the anion effect on the Sr-crown ether binding. 

However, as training i am trying to run a metadynamics with just one collective variable (distance between Sr and the COM of the crown ether) to compare the results with the ones i got from a previous umbrella sampling. 

The main problem is that i have prepared this plumes file: 

DUMPMASSCHARGE FILE=mcfile

C1: COM ATOMS=1-42

d1: DISTANCE ATOMS=43,C1

restraint: METAD ARG=d1 PACE=500 HEIGHT=1.5 BIASFACTOR=15 TEMP=300.0 SIGMA=0.1 FILE=HILLS GRID_min=0 GRID_MAX=2.6
UPPER_WALLS ARG=d1 AT=2.6 KAPPA=1000 EXP=2 EPS=1
PRINT ARG=d1,restraint.bias FILE=COLVARmeta STRIDE=500

but i am getting the following error: 

PLUMED:
PLUMED: (tools/Grid.cpp:168) PLMD::GridBase::index_t PLMD::GridBase::getIndex(const std::vector<unsigned int>&) const
PLUMED: Looking for a value outside the grid along the 0 dimension (arg name: d1)
PLUMED:
PLUMED: The above exception was the direct cause of the following exception:
PLUMED:
PLUMED: (core/PlumedMain.cpp:971) void PLMD::PlumedMain::justCalculate()
PLUMED: An error happened while calculating restraint

It seems like wall i am applying is not working.... 

Any suggestion/help would be really appreciated! Moreover,Is there is any tip to correctly choose the optimum height, width and biasfactor!?

Isaac

[Gareth Tribello]

Hello

You need to increase GRID_MAX on the METAD line.  The upper wall does not mean that the distance cannot be larger than 2.6 nm.  It means that there is a harmonic restraint that kicks in when the distance gets to 2.6.  If you increase that 2.6 to maybe 3.5 nm the problem will disappear.

I hope this helps

Gareth

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