[gmx-users] (no subject)

[Michael D. Daily]

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 
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.

--- lincs error ---

Step 1, time 0.002 (ps)  LINCS WARNING
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./
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
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

; cpt control
tcoupl                   = nose-hoover
tc-grps                  = System
tau_t                    = 0.4
ref_t                    = 300.0
Pcoupl                   = parrinello-rahman
pcoupltype               = isotropic
tau_p                    = 1.0
compressibility          = 4.5e-5
ref_p                    = 1.0

; velocity & temperature control
gen_vel                  = yes
gen_temp                 = 300.0
annealing                = no
constraints              = hbonds
;constraints              = none
constraint_algorithm     = lincs
;constraint_algorithm     = shake
morse                    = no

Mike

-- 
Michael D. Daily, Ph.D.
Postdoctoral Fellow
Qiang Cui group
Department of Chemistry
University of Wisconsin-Madison


-- 
Michael D. Daily, Ph.D.
Postdoctoral Fellow
Qiang Cui group
Department of Chemistry
University of Wisconsin-Madison

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