[gmx-users] Simulation explodes (protein-ligand-protein)

[Giovana Bergamini]

>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).

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