[gmx-users] Rerun same trajectory - Pulling

[Steven Neumann]

Thank you Justin.
It is weird I cannot reproduce it with the same mdp:

title       = Umbrella pulling simulation
define      = -DPOSRES_T
; Run parameters
integrator  = md
dt          = 0.002
tinit       = 0
nsteps      = 150000    ; 0.3 ns
nstcomm     = 10
; Output parameters
nstxout     = 0
nstvout     = 0
nstxtcout   = 100       ; every 1 ps 1500 frames
nstenergy   = 500
; Bond parameters
constraint_algorithm    = lincs
constraints             = all-bonds
continuation            = yes       ; continuing from NPT
; Single-range cutoff scheme
nstlist     = 5
ns_type     = grid
rlist       = 1.4
rcoulomb    = 1.4
rvdw        = 1.2
vdwtype     = Switch
rvdw-switch = 1.0
; 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
; Temperature coupling is on
tcoupl      = V-rescale                     ; modified Berendsen thermostat
tc_grps     = Protein LIG_Water_and_ions   ; two coupling groups - more accurate
tau_t       = 0.1   0.1                     ; time constant, in ps
ref_t       = 298   298                     ; reference temperature,
one for each group, in K
; Pressure coupling is on
Pcoupl          = Parrinello-Rahman
pcoupltype      = isotropic
tau_p           = 2.0
compressibility = 4.5e-5
ref_p           = 1.0
; 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     = GLU
pull_group1     = LIG
pull_rate1      = 0.01      ; 0.001 nm per ps = 1 nm per ns
pull_k1         = 2000      ; kJ mol^-1 nm^-2


Using:

grompp -f pull3nmSnew.mdp -c npt298.gro -p topol.top -n index.ndx -t
npt298.cpt -o pullS_2new.tpr

As I take velocities from npt it should be reproducible but profiles
force vs time looks similar with breaking point at different time.

Can I edit somehow tpr file and change the frequency of frames only?
Otherwise I have to run pulling again and US windows from scratch...
quite time consuming.

Steven



On Tue, Dec 25, 2012 at 1:28 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 12/25/12 3:51 AM, Steven Neumann wrote:
>>
>> Maybe I wrote it wrote it wrong.
>>
>> I have 1500 frames of which with 0.1 nm spacing I have chosen 14 to
>> run umbrella sampling windows.
>>
>> I used:
>>
>> conf0.gro
>> conf140.gro
>> conf213.gro
>> conf262.gro
>> conf263.gro
>> conf300.gro
>> ...
>> conf1500.gro
>>
>> However, the moment when my ligand became dettached is very short
>> (beween conf conf262.gro and 263.gro) that there is a gap in
>> histograms. So I need the same pulling trajectory but with more frames
>> e.g. 10 times higher.
>>
>> when I use grommp -f new.mdp -o new.tpr
>> mdrun -rerun oldPull.xtc -s new.tpr -deffnm new
>>
>> I dont get my new.xtc ... Hoiw can I solve it?
>>
>
> Because, as I said, that's not what the -rerun function does.  The -rerun
> function simple re-evaluates the energies of the existing frames according
> to the topology in the .tpr file, thus allowing you to re-calculate energy
> terms based on new energy groups or a modified topology.  If a frame does
> not exist, you cannot create it magically.  If you didn't save the frame you
> needed, you need to run a new simulation.  There is no way to interpolate
> new frames.
>
> -Justin
>
>
> --
> ========================================
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists