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I have been using a particular contacts.dat file for RNA simulation. I want to set the parameters from contacts.dat file directly in main() using Molmodel functions.

I was able to figure out the relevant functions for most of the commands in contacts.dat file in the class SimTK::DuMMForceFieldSubsystem. There is one command for which i could not find the equivalent function.

1) The command is,
leontisWesthofInFileName Base-interaction-parameters.4.csv

How do i set this directly in main() ?

2) Also, I have the following two commands

setTemperature 1
temperature 300 1

in my contacts.dat file. To include this, I have added the following two lines in main().

GeneralForceSubsystem Fsub(system);
Force::Thermostat(Fsub, matter,SimTK_BOLTZMANN_CONSTANT_MD,300,100);

Is this equivalent to the commands in contacts.dat file ?

Where i am headed with this: At this point, I can simulate coarse grain RNA chains without using the Simbody Integrators. Right now, I am attempting to reproduce the results for a particular RNA simulation of interest to us which was originally done using RNABuilder. For this, I have to set the MD simulation parameters manually from the contacts.dat file and then perform time-stepping using the solver i wrote.

I can always edit the runDynamics() function in Repel.h for this. However, it is preferable if I can simply call pre-compiled functions, instead of actively editing the source, which is what we have been doing till date.

Thanks,
Kishor Bhalerao

sorry, i am only now becoming aware that i was not set up to monitor this forum.

leontisWesthofInFileName has no equivalent in molmodel. It contains the parameters for the base pairing interactions, which are entirely in RNABuilder.

For the thermostat, yes, you are making the same instantiation.

Let me know if you are still working on this and need further help; we can do skype or phone as well. On skype I"m samuelfloresc .. remember i'm on european time now.