[gmx-users] Orienting molecule in a correct direction

[faride badalkhani]

Hi,

You're right. I am sorry for the unclear explanation. I used the editconf
-princ command and chose ligand as the group for aligning in x direction.
then I used the editconf -rotate 0 90 0 to align along z. Then I executed
pdb2gmx command. Then
editconf -f complex.gro -o complex-box.gro -center 4 4 4 -box 8 8 24
I want to pull a total distance of 16 nm.
I continued the procedure till generating configurations and this is the
mdp file for pulling:

title       = Umbrella pulling simulation
define      = -DPOSRES_A
; Run parameters
integrator  = md
dt          = 0.002
tinit       = 0
nsteps      = 1000000    ; 1 ns
nstcomm     = 50
; Output parameters
nstxout     = 5000       ; every 10 ps
nstvout     = 5000
nstfout     = 5000
nstxtcout   = 5000       ; every 1 ps
nstenergy   = 5000
; Bond parameters
constraint_algorithm    = lincs
constraints             = all-bonds
continuation            = yes       ; continuing from NPT
; Single-range cutoff scheme
nstlist     = 5
ns_type     = grid
rlist       = 1.2
rcoulomb    = 1.2
rvdw        = 1.2
; PME electrostatics parameters
coulombtype     = PME
fourierspacing  = 0.12
fourier_nx      = 0
fourier_ny      = 0
fourier_nz      = 0
pme_order       = 4
ewald_rtol      = 1e-5
optimize_fft    = yes
; Berendsen temperature coupling is on in two groups
Tcoupl      = Nose-Hoover
tc_grps     = Protein_CHL  Water_and_ions
tau_t       = 0.5       0.5
ref_t       = 310       310
; Pressure coupling is on
Pcoupl          = Parrinello-Rahman
pcoupltype      = isotropic
tau_p           = 1.0
compressibility = 4.5e-5
ref_p           = 1.0
refcoord_scaling = com
; Generate velocities is off
gen_vel     = no
; Periodic boundary conditions are on in all directions
pbc     = xyz
; Long-range dispersion correction
DispCorr    = EnerPres
; Pull code
pull                    = umbrella
pull_geometry           = distance      ; simple distance increase
pull_dim                = N N Y
pull_start              = yes           ; define initial COM distance > 0
pull_ngroups            = 1
pull_group0             = Chain_A
pull_group1             = Chain_B
pull_rate1              = 0.1           ; 0.1 nm per ps
pull_k1                 = 836.8         ; kJ mol^-1 nm^-2

but ater 60000 steps I got the following error:

Distance of pull group 1 (11.850665 nm) is larger than 0.49 times the box
size 12.092276)

Should I increase all the box dimensions or just z dimension?


Regards,
Farideh


On Sun, Oct 30, 2016 at 7:50 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 10/30/16 12:03 AM, faride badalkhani wrote:
>
>> Dear all,
>>
>> I want to define z axis as the reaction coordinate in a series of umbrella
>> sampling simulations. As a first step, I use the editconf -prince to
>> orient
>> the ligand along the x axis and then I change the x and z columns in an
>>
>
> x and z columns of what?  If you have an orientation aligned along x, and
> you want it aligned along z, it's a simple use of editconf -rotate 0 90 0
>
> editor. But, every time I get error at pulling step. Could you tell me what
>> is wrong?
>>
>
> No, because you haven't told us what the exact error is and all the steps
> you took in between.  There's a lot of work that goes on between setting up
> an orientation and actually running a simulation.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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