[obasekia]

Reducing the number of cores to 24  as you suggested helped to speed things up but i really don’t understand why(atdyn for implicit solvent). also just an unrelated question. i started GaMD simulation with implicit solvent but i cannot use NPT and the time step of 4fs with hydrogen mass partition hope it wont fact the simulation

[obasekia]

Also you other question i am using double precision. i should also say 24 cores a 500ps takes approximately 7-8hrs though

[obasekia]

Thanks I will try that and give feedback. But I thought increasing number of cores should speed up the simulation?

[obasekia]

Thanks, i will check it out. my other question is, how do you check for convergence in GaMD?

[obasekia]

Thanks that means i can use atdyn rather than spdyn for the simulation of GaMD?

[obasekia]

Thanks checked my log file i can see MPI compiler = NO MPI does that mean i complied genesis without mpi?

[obasekia]

I tried it again and i got an error about

WARNING: too long bond: 6200 6199 2.87516
Setup_Fitting_Spdyn> NO fitting is applied, skip
fitting method = NO

Memory allocation error rank_no = 1
Memory allocation error rank_no = 2
Memory allocation error rank_no = 3
Memory allocation error rank_no = 0

[obasekia]

Thanks for the explanation

[obasekia]

How do you determine the final_rmsd AND is the reference value in the tutorial always 4.3 irrespective of the protein?

[obasekia]

Thanks for the reply

[obasekia]

Sorry it was about using Gaussian Accelerated MD simulation. Choice of using sigma0_dih and sigma0_pot. Tutorial 12.4

[obasekia]

Thanks

[obasekia]

Thank you. please i asked a question about Gaussian accelerated molecular dynamics in the forum and will be happy if i can get a reply