On 12/17/17 8:22 AM, Faezeh Pousaneh wrote:
Dear Justin,
How can I check that ''input configuration is "broken" across PBC'' ?
From vmd it is hard to say, since I only have one component system.
What is that one component? If a group of atoms is supposed to be in a
charge group, and it is split across the box, then you need to correct
it with trjconv or (if you are absolutely sure this isn't a problem)
override with grompp -maxwarn (dangerous and generally not wise).
-Justin
Best regards
On Fri, Dec 15, 2017 at 2:05 PM, Faezeh Pousaneh <fpoosa...@gmail.com>
wrote:
The sum of the two largest charge group radii (7.984601) is larger than
rlist (0.347900).
the configuration looks fine across pbc. Everything looks normal.
Following is my md. I have user-specified potential so I need to have
cut-off values as given below.
integrator = md
dt = 0.001
nsteps = 3000000
nstxout = 100000 ; save coordinates every 0 ps
nstvout = 100000 ; save velocities every 0 ps
nstlog = 100000 ; update log file every
nstenergy = 100000 ; save energies every
nstxtcout = 100000 ; Output frequency for xtc file
xtc-precision = 100000 ; precision for xtc file
ns_type = grid ; search neighboring grid cells
nstlist = 10 ; fs
pbc = xyz ; 3-D PBC
rlist = 0.3479 ; short-range neighborlist cutoff
(in nm)
rcoulomb = 0.3479 ; short-range electrostatic
cutoff (in nm)
rvdw = 0.3479; short-range van der Waals cutoff (in nm)
coulombtype = PME-user ; Particle Mesh Ewald for
long-range electrostatics
pme_order = 4 ; cubic interpolation
fourierspacing = 0.16 ; grid spacing for FFT
vdw-type = user
Tcoupl = berendsen ; modified Berendsen thermostat
tc-grps = co2 rest ; two coupling groups -
more accurate
tau_t = 0.1 0.1 ; time constant, in ps
ref_t = 179.8 179.8 ; reference temperature, one
for each group, in K
;tc-grps = system
cutoff-scheme =group
energygrps = co2 rest
Pcoupl = no;Parrinello-Rahman
Pcoupltype = Isotropic
tau_p = 1.0
compressibility = 6.2e-5
ref_p = 50.0
gen_vel = yes
gen_temp = 179.8
gen_seed = 712349
DispCorr =no; EnerPres ; account for cut-off vdW
scheme
constraints = all-bonds ; all bonds constrained (fixed
length)
continuation = no ; Restarting after NPT
constraint-algorithm = lincs ; holonomic constraints
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
Best regards
On Fri, Dec 15, 2017 at 1:44 PM, Justin Lemkul <jalem...@vt.edu> wrote:
On 12/15/17 4:26 AM, Faezeh Pousaneh wrote:
Hi,
I get this error only in NVT equlibration step, not in the NPT and
production steps. Should I worry about it?
In gromacs page it tell the error can come from 4 reasons, but how I can
recognize which can be mine?
Check the size of your largest charge group, value of rlist, or whether
or not the input configuration is "broken" across PBC.
-Justin
http://www.gromacs.org/Documentation/Errors?highlight=docume
ntation#The_sum_of_the_two_largest_charge_group_radii_(X)
_is_larger_than.c2.a0rlist_-_rvdw.2frcoulomb
Best regards
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
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Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
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