[gmx-users] Hydroxyl bonds rotating too much

[Juan José Galano Frutos]

For more details, my system also has another cofactor with similar
characteristics (FAD), I mean with hydroxyl groups but all is going fine
with it so far (equilibration step).

As I wrote before I did the following steps:
1- vaccuum minimization
2- solvating
3- neutralizing
4- minimization
5- heating (increases by temperature ramp and using position restraints for
all the components of the system)
6- equilibration (3 sequencial steps: the first step (NVT with a v-rescale
thermostat) is where the system crashes)

here the .mdp file of this first equilibration step:

define              =

integrator          = md
dt                     = 0.001  ; ps !
nsteps              = 150000 ; 150 ps
nstcomm          = 1
nstxtcout          = 10000
xtc-precision     = 10000
nstxout             = 0
nstvout             = 0
nstfout              = 0
nstlog               = 10000
nstenergy          = 10000

; Non-bonded Interactions
nstlist               = 10
ns_type            = grid
rlist                  = 0.9
coulombtype     = PME
rcoulomb          = 0.9
vdwtype           = cut-off
rvdw                 = 0.9
vdw-modifier     = Potential-shift-Verlet

; Berendsen temperature coupling is on in two groups
Tcoupl              =  v-rescale
tc-grps             =  System
tau_t                =  0.1
ref_t                 =  310

; Energy monitoring
energygrps        =  System
DispCorr            =  EnerPres

; Isotropic pressure coupling is now off
Pcoupl              =  no
Pcoupltype        =  isotropic
tau_p                =  5.0
compressibility   =  4.6e-5
ref_p                 =  1.0

; Generate velocites is off at 310 K
gen_vel              =  no
gen_temp           =  310
gen_seed           =  -1

; Constraints
constraint_algorithm = lincs
lincs_order           = 8
constraints           = all-bonds
lincs-warnangle     = 60
disre                    = simple



Thank you in advance

Best regards

Juan José




2017-05-16 13:03 GMT+02:00 Juan José Galano Frutos <juanjogf at gmail.com>:

> Hi there:
>
> I am simulating a protein which include as a cofactor a molecule bearing
> some hydroxyl groups. The system is crashing from the begining of the
> equilibration step (after the following steps: vaccuum minimization,
> solvating, neutralizing, minimization, heating) due to -in all the
> replicas- to hydroxyl bonds that steadily rotated more than 60 and even 90
> degrees.
> I checked the structures and the systems looking for either water or
> protein parts in so close contact with this hydroxyl groups, but it was not
> the case. Then I proceeded to re-minimize again the systems after the
> heating step and afterward to relaunch the equilibration step, but again
> the same happened. I also checked the topology file of this cofactor but
> all seems to be fine, I mean charges.
> Then, what could be happening? Is it common this behaviour in hydroxyl
> groups?Any help please....
>
> Thanks
>
> Best
>
> Juan José Galano Frutos
>
> Department of Biochemistry and
> Molecular and Cellular Biology,
> Faculty of Sciences,
> University of Zaragoza
> Pedro Cerbuna # 12, 50009
> Zaragoza (Spain)
> +34 976 76 28 06 <+34%20976%2076%2028%2006>
>
> Institute for Biocomputation and
> Physics of Complex Systems (BIFI)
> Mariano Esquillor, Edificio I + D - 50018
> Zaragoza (Spain)
>