[gmx-users] Test Particle Insertion of Water
Javier Cerezo
jcb1 at um.es
Wed May 9 16:16:06 CEST 2012
The trr file has something wrong. Look at "Coords", it has 0 frames
You may have forgotten to set nstxout to a non-zero value?
Javier
El 09/05/12 16:10, Steven Neumann escribió:
> 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
> <mailto: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
> <mailto: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
>> <mailto: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 <tel:%28%2B34%29868887434>
>>
>> --
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>>
>>
>>
>>
>
> --
> Javier CEREZO BASTIDA
> PhD Student
> Physical Chemistry
> Universidad de Murcia
> Murcia (Spain)
> Tel: (+34)868887434 <tel:%28%2B34%29868887434>
>
> --
> gmx-users mailing list gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
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> 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
> <mailto:gmx-users-request at gromacs.org>.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
>
>
>
--
Javier CEREZO BASTIDA
PhD Student
Physical Chemistry
Universidad de Murcia
Murcia (Spain)
Tel: (+34)868887434
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