Giovana Bergamini wrote:
Hi!
We have a problem with a protein-ligand-protein simulation. It is a somewhat
large system (approx. 360 amino acid residues with approx. 70 monosaccharides),
that requires a larger box for proper simulation.
We used exclusions (especifically for the problematic atoms) and restrictions
(tested values of 5000, 2000, 1000 - for backbone and for monosaccharides),
both combined and individually, and when they were kept for the entire
simulation, it went just fine. But when these restrictions and exclusions were
removed, the glycan portion, that isn’t connected to any of the proteins
“explodes”.
Any suggestions?
Thank you in advance,
Hi,
We used the gromos43a1 force fied, and the .mdp with minimization parameters
with no restraints or exclusions were:
title = Yo
cpp = /lib/cpp
define = -DFLEX
constraints = all-bonds
integrator = md
tinit = 0000
dt = 0.0005 ; ps !
nsteps = 2000000 ; total 00000-1000 ps.
nstcomm = 1
nstxout = 250
nstvout = 1000
nstfout = 0
nstlog = 100
nstenergy = 100
nstlist = 10
ns_type = grid
coulombtype = PME
rlist = 0.9
rcoulomb = 0.9
rvdw = 0.9
fourierspacing = 0.12
optimize_fft = yes
pme_order = 4
ewald_rtol = 1e-5
; Berendsen temperature coupling is on in four groups
Tcoupl = berendsen
tc-grps = Protein_1 Protein_2 gli_1 gli_2 gli_3 gli_4 gli_5 CA+
tau_t = 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1
ref_t = 50 50 50 50 50 50 50 50
; Energy monitoring
energygrps = Protein_1 Protein_2 gli_1 gli_2 gli_3 gli_4 gli_5 CA+
; Isotropic pressure coupling is now on
Pcoupl = berendsen
Pcoupltype = isotropic
tau_p = 0.5
compressibility = 4.5e-5
ref_p = 1.0
; Generate velocites is off at 100 K.
gen_vel = yes
gen_temp = 10.0
gen_seed = 173529
This .mdp file works fine without water, but when we include "sol" the
simulation explodes, too.
The tc-grps in this case are a glycoprotein (protein-1, gli_1, gli_2, gli_3,
gli_4 and gli_5) and a secondary protein (protein-2).
Are each of these groups sufficiently large to justify their own temperature
coupling group? I'd be especially concerned about coupling ions alone
(presumably there are only a few CA+?)
http://www.gromacs.org/Documentation/Terminology/Thermostats
If you can identify that certain molecules are unstable, then I'd suspect as
well that there might be problems with the topology. How did you generate it?
How did you validate the parameters? Do simulations of the sugar moieties alone
(using your topology) run stably?
-Justin
thank you again,
Giovana Bergamini
Faculdade de Farmácia
Grupo de Bioinformatica Estrutural
Universidade Federal do Rio Grande do Sul
Av. Bento Gonçalves, 9500
Prédio 43431, sala 202
CEP 91500-970, CP 15005, Porto Alegre, RS, Brazil
tel.: +55 51 3308 7770
http://www.cbiot. ufrgs.br/ bioinfo
--------------------------------------------------------------------
Centro de Biotecnologia da Universidade Federal do Rio Grande do Sul
--
========================================
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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