Michael D. Daily wrote:
Hi all,
I'm trying to run implicit solvent calculations in gromacs 4.5 with the
charmm forcefield. I am able to minimize successfully and compile for
When troubleshooting, it is always advisable to try the latest version (4.5.4)
to see if the problem is reproducible. If a pertinent bug has been fixed,
there's no use troubleshooting the broken version.
mdrun, but soon after starting, mdrun complains about excessive rotation
in LINCS (see the error printed below that). I also include my mdp file
at the bottom. Can anyone advise me as to the possible cause of such
errors, as it is difficult to diagnose given that grompp worked fine.
For reference:
http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System
If grompp worked, that just means your coordinate and topology matched and there
were no internal conflicts within the .mdp file. It is no guarantee that the
resulting simulation will actually work, unfortunately.
--- lincs error ---
Step 1, time 0.002 (ps) LINCS WARNING
Typically an instant LINCS failure indicates insufficient minimization. You
said you minimized successfully, but what does this mean? What values did you
achieve for Fmax and Epot?
relative constraint deviation after LINCS:
rms 0.000780, max 0.020692 (between atoms 880 and 881)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
606 607 36.7 1.0527 0.1080 0.1080
614 615 35.6 0.8972 0.1125 0.1111
614 616 75.3 0.1054 0.1121 0.1111
880 881 58.0 0.1068 0.1134 0.1111
880 882 50.4 0.9168 0.1121 0.1111
889 890 55.3 0.1066 0.1122 0.1111
889 891 35.3 0.8588 0.1118 0.1111
---- mdp file ------------
; title and include files
title = 1EX6-S35P_md1
cpp = cpp
include =
-I/home/yoo2/myusr/gromacs-3.3.3/share/gromacs/top/ -I./
Any reason you're including files from an ancient Gromacs version?
define =
; integrator and input/output setting up
integrator = md
nsteps = 1000000 ; 2 ns
;nsteps = 5000 ; 2 ns
dt = 0.002
nstxout = 5000
nstvout = 5000
nstenergy = 500
nstxtcout = 500
nstlog = 500
xtc_grps = System
energygrps = System
comm_mode = Linear
;implicit solvent
implicit_solvent = GBSA
gb_algorithm = Still
gb_saltconc = 0.15
FYI, gb_saltconc is nonfunctional. Don't expect it to do anything :)
rgbradii = 1.0
; neighbor searching and vdw/pme setting up
nstlist = 10
ns_type = grid
pbc = xyz
;rlist = 1.4
rlist = 1.0
;coulombtype = pme
coulombtype = Cut-Off
fourierspacing = 0.1
pme_order = 6
;rcoulomb = 1.4
rcoulomb = 1.1
;vdwtype = switch
vdwtype = Cut-Off
rvdw_switch = 1.0
;rvdw = 1.2
rvdw = 1.1
All of these are potentially problematic. Running implicit simulations
typically requires longer cutoffs than would normally be needed for explicit
solvent simulations. Try rlist=rvdw=rcoulomb=2.0 nm.
; cpt control
tcoupl = nose-hoover
A better choice for initial equilibration would be either V-rescale or
Berendsen. I know this can be an issue in explicit solvent, when velocities can
oscillate a lot at the outset of a simulation using Nose-Hoover and the
simulation box can explode; I don't know if this is such a big deal with
implicit, but it can't hurt to try.
tc-grps = System
tau_t = 0.4
ref_t = 300.0
Pcoupl = parrinello-rahman
I don't know how an implicit box will respond to pressure coupling, but it would
be better to try NVT first and see if it's stable, then try NPT and see if
things break down.
One option that might be advantageous is to use the all-vs-all kernels for a
speed upgrade. You can accomplish this with:
rlist = 0
nstlist = 0
rvdw = 0
rcoulomb = 0
rgbradii = 0
pbc = no
comm-mode = angular
You'd have to run with mdrun -pd (particle decomposition), but the end result
can be quite fast and you avoid potential periodicity effects.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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