[gmx-users] Test Particle Insertion of Water

Steven Neumann s.neumann08 at gmail.com
Wed May 9 16:10:02 CEST 2012 

I added one water molecule in my topology to all water molecules:

[ molecules ]
; Compound        #mols
Alanine            40
SOL               724

Maybe I should add aditional line like:

[ molecules ]
; Compound        #mols
Alanine            40
SOL               723
SOL                  1

What do you think?


On Wed, May 9, 2012 at 3:04 PM, Steven Neumann <s.neumann08 at gmail.com>wrote:

> 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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