Open fercofas opened 10 months ago
Did you modify the Martini 3 itp
file as described in the basic protein tutorial, section B2?
In addition, you should define the variable GO_VIRT
at the beginning of the topology file:
#define GO_VIRT
such that the modifications are active and the virtual beads are defined by gmx grompp
.
Yeah, It worked. Thank you very much. I added the corresponding lines to Martitin 3 itp. The variable GO_VIRT was already in the topology file. I suggest this info should be included here because this phrase in the tutorial "Because the main Martini force field .itp should not be changed" is a bit misleading. I'll be testing the protocol with structures with more than one chain.
I've been able to get the files expected in step 3.2 with the basic usage instructions. Nonetheless, while implementing system minimization, I discovered the issue depicted in the enclosed image.
Is it necessary to take any additional steps in order to carry out the simulation?
Additional information: The in-house Python script generates an itp file that contains the information on both molecules_BB-part-def_VirtGoSites and molecules_0_go-table_VirtGoSites itp files, as well as another itp file that is similar to molecule_0.itp.