GROMACS version: 2021 (beta version constant pH)
GROMACS modification: No
Hi everyone,
Thanks for your interest, I am here to ask some questions about the beta version of gromacs doing constant pH MD, here the repository: Gromacs constant ph · GitLab
I am on the tutorials and I am having a doubt on wheter and also how to put position restraints flags -DPOSRES and -DPOSRES_BUF in the .mdp file during the minimization and then the equilibration in both nvt and npt ensembles, this in both the “parametrisation” and the “sampling” folders. Let’s just stick to the 1st tutorial, the simplest.
If using 1 buffer particle, I see that I have to use a specific posre.itp file indicating just one atom through the “parametrisation” step, and both the reported flags in all the .mdp files of minimization and nvt and npt equilibration. Thus, the typical posre.itp which is generated after the first instruction of the tutorial returning the first .gro file has to be substituted by that abovementioned posre.itp; it means that, concerning the system, only one of its atoms is restrained, not the whole of them as I usually saw in various system preparations. Right?
If one decides to use 10 buffer particles, instead, I do not have to restraint the distances of the BUF particles from the titratable site. Then, what do I have to change in the “parametrisation” steps? I will explain: I would comment solely the -DPOSRES_BUF flag in all the .mdp files in which it appears, and also comment the -DPOSRES in the npt.mdp file in analogy with what I see in the other step, the “sampling” one. Is this correct? And what posre.it should I use this time? That produced automatically from the first instruction of the tutorial, i.e. the one restraining all the atoms of the tripeptide and generated by this instruction " gmx pdb2gmx -f 0_asp.pdb -o 1_asp.gro -p -ignh -ter "? Or should I avoid using any posre.itp at all, commenting also both the two flags?
In the case of 10 buffer particles, is then the “sampling” folder the same in terms of .mdp files of the case in which I use 1 BUF particle (in the “sampling” folder, too)? In that case, will both the 10 and 1 BUF(s) cases use the posre.itp file automatically generated from the " gmx pdb2gmx -f 0_asp.pdb -o 1_asp.gro -p -ignh -ter " instruction, i.e. the one restraining all the atoms of the system?
I asked 8 questions and please ask for 8 different answer, I beg you not to skip one, otherwise the picture won’t be clear to me. Thanks in advance for the help!!
Best Regards,
Jacopo