>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 isnt 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 =
dt = 0.0005 ; ps !
nsteps = 200 ; total 0-1000 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).
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
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