GROMACS modification: Yes/No
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Dear GROMACS community
I would like to accelerate the sampling using the REST2 I am following the instruction based on the REST2 tutorial
1- I need to edit the topology file produced by using grompp -pp
2- I need to change the [ atoms] section to select HOT atoms by adding () sign.
[ atoms ] ;nr type resnr residue atom cgnr charge mass typeB chargeB massB ;residue
1 HC 1 ACE HH31 1 0.112300 1.0080 ;qtot 0.1123
2 CT_ 1 ACE CH3 2 -0.366200 12.0100 ;qtot -0.2539
3- The modified typology needs to be scaled at each λ value. Plumed comes with a partial tempering command-line tool that can be used to generate scaled topology, which will scale the force fields parameters of the section [ atom type ] of a given topology file.
4- Use grompp commands to generate gromacs binary input file (tpr).
I am struggling with step number 4,
I got this error ( ERROR 1 [file scaled2.top, line 233490]:
Atomtype 2C_ not found)
I have two questions:
How to solve this error?
How to generate different topologies corresponding to each λ value ( replicas) because I need to process these topology files?