[gmx-users] Test Particle Insertion of Water

Steven Neumann s.neumann08 at gmail.com
Wed May 9 16:04:28 CEST 2012


Checking file md.trr
trn version: GMX_trn_file (single precision)
Reading frame       0 time    0.000
# Atoms  2569
Last frame       2000 time 100000.000


Item        #frames Timestep (ps)
Step          2001    50
Time          2001    50
Lambda        2001    50
Coords           0
Velocities    2001    50
Forces           0
Box           2001    50

Well, it looks ok. Any suggestions?

On Wed, May 9, 2012 at 3:01 PM, Javier Cerezo <jcb1 at um.es> wrote:

>  Sorry, I saw now the command line you've posted. Did you check your trr
> with gmxcheck?
>
>
> El 09/05/12 15:49, Steven Neumann escribió:
>
> 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
>>
>> --
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>>
>
>
>
>
> --
> Javier CEREZO BASTIDA
> PhD Student
> Physical Chemistry
> Universidad de Murcia
> Murcia (Spain)
> Tel: (+34)868887434
>
> --
> 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
>
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