[gmx-users] problems with pull code on Martini CG
gmx3 at hotmail.com
Thu Apr 11 08:48:51 CEST 2019
You should not use direction-periodic, you don't want to pull more than half the box size, I presume.
Your pull rate is extremely high 50 nm/ns. I would start by lowering this.
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Bennett Addison <baddison at sdsu.edu>
Sent: Thursday, April 11, 2019 12:50 AM
To: gmx-users at gromacs.org
Subject: [gmx-users] problems with pull code on Martini CG
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
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 = yes
pull_ncoords = 1 ; only one reaction coordinate
pull_ngroups = 2 ; two groups defining one reaction
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
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
- 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?
Dr. Bennett Addison
Manager, SDSU NMR Facility
baddison at sdsu.edu
206-235-5415 <//206-235-5415> (cell)
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