Hello gromacs users, I am fairly new to MD, trying hard to troubleshoot this issue myself before posting. But I am at a loss.
I am trying to simulate pulling on a large protein, using Martini CG simulations and adding the pull code. I am following tutorials for umbrella sampling (all atom) and for martini protein simulations. Basically, the exact same setup procedure works when the box size is small, but when I scale up, things get screwy. For example: 200 AA protein, placed 50 x 12 x 12 box and pull along X (see pull code below: using direction-periodic geometry, pull along vector -1.0 0.0 0.0) gmx editconf -f CG.pdb -o newbox.gro -box 50 12 12 -center 7 6 6 Followed by minimization in vac, solvate, minimize, equilibrate, then create groups with gmx make_ndx, assign Chain_A as anchored residue, assign Chain_B as residue to pull, make sure position restraints are correct, and finally setup and run md_pull.mdp. This simulation works great. I see a nice unfolding using martini CG model. Pull code: ; Pull code pull = yes pull_ncoords = 1 ; only one reaction coordinate pull_ngroups = 2 ; two groups defining one reaction coordinate pull_group1_name = Chain_A pull_group2_name = Chain_B pull_coord1_type = umbrella ; harmonic potential pull_coord1_geometry = direction-periodic ; pull_coord1_vec = -1.0 0.0 0.0 pull_coord1_groups = 1 2 pull_coord1_start = yes ; define initial COM distance > 0 pull_coord1_rate = 0.05 ; 0.05 nm per ps = 5 nm per ns pull_coord1_k = 1000 ; kJ mol^-1 nm^-2 Now when I try to replicate the exact same setup but using a larger box (100nm 20nm 20nm) everything fails. When I visualize the trajectory my protein does not appear to be pulled, but the position output pullx.xvg shows increase in distance, pullf.xvg shows no changes in force, and if I plot distance between Chain_A and Chain_B using gmx distance, I see an expected distance increase. DOES NOT WORK: gmx editconf -f CG.pdb -o new box.gro -box 100 20 20 -center 8 10 10 (pullx looks ok, but pullf is flat, protein does not extend) WORKS: gmx editconf -f CG.pdb -o new box.gro -box 50 12 12 -center 5 6 6 (trajectory looks great, pullf and pullx as expected) Every other parameter / setup procedure is the same, just box size is different. I need a larger box on my bigger protein (200 AAs) because it will fully extend past 50nm. I have tried with two configurations, same issues - gromacs version 5.1.5 on a computing cluster, single node, AMD with 32 cores - gromacs version 2018.3 on local machine with intel xeon E5 processors, 40 cores with GPU acceleration Does anybody know why this may be happening, and how I can get around it? Thank you! -Bennett ________________________ Dr. Bennett Addison Manager, SDSU NMR Facility baddi...@sdsu.edu 206-235-5415 <//206-235-5415> (cell) -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.