[gmx-users] Test Particle Insertion of Water
Steven Neumann
s.neumann08 at gmail.com
Wed May 9 16:22:32 CEST 2012
Thank you! I have missed it somehow. I can still use my xtc trajectory.
Steven
On Wed, May 9, 2012 at 3:16 PM, Javier Cerezo <jcb1 at um.es> wrote:
> 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>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
>>>> Please search the archive at
>>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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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
>>>
>>
>>
>
>
>
> --
> 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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