[gmx-users] Test Particle Insertion of Water

[Steven Neumann]

hello gmx users,

I am sorry for bothering you but I was searching mailing list and no
results. I have a problem with my test particle insertion as I run the
workflow I described previously with my mdp:

title       = Test Particle Insertion
; Run parameters
integrator  = tpi
nsteps      = 50000000    ; 100 ns
dt          = 0.002     ; 2 fs
; Output control
nstxout     = 0          ; suppress .trr output ; output coordinates every
25 ps
nstvout     = 25000     ; velocities to output every 25000 steps
nstenergy   = 1000      ; save energies every 2 ps
nstlog      = 1000      ; update log file every 2 ps
nstxtcout   = 100000         ; suppress (tlumic) xtc trajectory
energygrps  = System
continuation    = no           ; first dynamics run
constraint_algorithm = lincs    ; holonomic constraints
constraints     = all-bonds     ; all bonds (even heavy atom-H bonds)
constrained
lincs_iter      = 1             ; accuracy of LINCS
lincs_order     = 4             ; also related to accuracy
; Neighborsearching
ns_type     = grid      ; search neighboring grid cells
nstlist     = 5         ; 10 fs
vdwtype     = Switch
rvdw-switch = 1.0
rlist       = 1.4       ; short-range neighborlist cutoff (in nm)
rcoulomb    = 1.4       ; short-range electrostatic cutoff (in nm)
rvdw        = 1.2       ; short-range van der Waals cutoff (in nm)
ewald_rtol  = 1e-5      ; relative strenght of the Ewald-shifted potential
rcoulomb
; Electrostatics
coulombtype     = PME       ; Particle Mesh Ewald for long-range
electrostatics
pme_order       = 4         ; cubic interpolation
fourierspacing  = 0.12      ; grid spacing for FFT
; Temperature coupling is on
tcoupl      = V-rescale                     ; modified Berendsen thermostat
tc_grps     = System                 ; two coupling groups - more accurate
tau_t       = 0.1                             ; time constant, in ps
ref_t       = 318                         ; reference temperature, one for
each group, in K
; Pressure coupling is on
pcoupl      = Parrinello-Rahman             ; pressure coupling is on for
NPT
pcoupltype  = isotropic                     ; uniform scaling of box vectors
tau_p       = 2.0                           ; time constant, in ps
ref_p       = 1.0                           ; reference pressure, in bar
compressibility = 4.5e-5                    ; isothermal compressibility of
water, bar^-1
; Periodic boundary conditions
pbc         = xyz       ; 3-D PBC
; Dispersion correction
DispCorr    = EnerPres  ; account for cut-off vdW scheme
; Velocity generation
gen_vel     = yes       ; assign velocities from Maxwell distribution
gen_temp    = 318       ; temperature for Maxwell distribution
gen_seed    = -1        ; generate a random seed

Then My log file:


 The temperature for test particle insertion is 318.000 K

Started Test Particle Insertion on node 0 Wed May  9 14:18:18 2012

Will insert 3 atoms with partial charges

Will insert 50000000 times in each frame of md318.trr
Will use the same neighborlist for 5 insertions in a sphere of radius
0.050000

  <V>  =         -nan nm^3
  <mu> =         -nan kJ/mol
No MEGA Flopsen this time

     R E A L   C Y C L E   A N D   T I M E   A C C O U N T I N G

 Computing:         Nodes     Number     G-Cycles    Seconds     %
------------------------------
-----------------------------------------
 Rest                   4                   5.218        1.9   100.0
-----------------------------------------------------------------------
 Total                  4                   5.218        1.9   100.0
-----------------------------------------------------------------------

    Parallel run - timing based on wallclock.

               NODE (s)   Real (s)      (%)
       Time:      0.485      0.485    100.0
               (Mnbf/s)   (MFlops)   (steps/hour)
Performance:      0.000      0.000            0.0
Finished mdrun on node 0 Wed May  9 14:18:19 2012



Files are empty. Do you have any clue what is happening?

Thank you for your time,

Steven


On Wed, May 9, 2012 at 1:45 PM, Javier Cerezo <jcb1 at um.es> wrote:

>  Hi Steven
>
> As I remember, TPI is based on the calculation of the potential at every
> conformation from the already computed simulation (inserting the particle
> in every snapshot), so velocities are not used.
>
> Anyway, use both and see if there are any differences.
>
> Javier
>
> El 09/05/12 11:27, Steven Neumann escribió:
>
> Dear Gmx Users,
>
> I am running TPI of the water in the system containing free amino acids.
> Steps:
>
> 1. I run the NPT simulation of 100 ns to equilibrate the system.
> 2. I added 1 extra water molecule to the final pdb file (converted from
> gro) and to topology
> 3. I creaded tpi.tpr using grompp using new pdb file with extra water
> molecule
> 4. mdrun –s tpi298.tpr -rerun md298.trr -deffnm tpi298 -tpi tpi298.xvg
> -tpid tpid298.xvg
>
> My question: Is it better generate new velocities in my mdp file
> (continuation = yes, gen_vel = no, tpi integrator) for a pdb file or use
> velocities from previous simulations (gro file)?
> If the second option is more appropriate what velocity shall I adjust to
> the extra water molecule?
>
> I will appreciate your reply.
>
> Steven
>
>
>
> --
> Javier CEREZO BASTIDA
> PhD Student
> Physical Chemistry
> Universidad de Murcia
> Murcia (Spain)
> Tel: (+34)868887434
>
> --
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