[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
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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>> www interface or send it to gmx-users-request at gromacs.org.
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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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