[gmx-users] the box lengths
Tsjerk Wassenaar
tsjerkw at gmail.com
Tue Jun 15 06:27:34 CEST 2010
Hi,
Which version of gromacs was this again? There have been issues with
pdb files being written without box (CRYST1) records, recorded in the
archive. Check the output .pdb files, especially after calling genbox
(grep "^CRYST1" file.pdb). Also, try the sequence always writing .gro
files as output.
Hope it helps,
Tsjerk
On Tue, Jun 15, 2010 at 6:12 AM, #ZHAO LINA# <ZHAO0139 at e.ntu.edu.sg> wrote:
> Hi,
>
> That's very nice all of you. I was just worried that so many details would make things blur.
>
>
> pdb2gmx -f try2.pdb -o try2.gro -ignh
>
> then choose ffG53a6,
>
> below is the minim.mdp going to be used (more than once).
> //////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
> ; Define can be used to control processes
> define = -DFLEXIBLE
>
> ; Parameters describing what to do, when to stop and what to save
> integrator = steep
> emtol = 1.0
> nsteps = 500
> nstenergy = 1
> energygrps = System
>
> ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions
> ns_type = simple
> coulombtype = cut-off
> rcoulomb = 1.0
> rvdw = 1.0
> constraints = none
> pbc = no
> ///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
>
> grompp -f minim.mdp -c try2.gro -p topol.top -o try2-vacuum.tpr
> mdrun -deffnm try2-vacuum -c try2-vacuum.pdb
>
> below is the mdrun results:
> ///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
> Reading file try2-vacuum.tpr, VERSION 4.0.7 (single precision)
> Steepest Descents:
> Tolerance (Fmax) = 1.00000e+00
> Number of steps = 500
>
> Stepsize too small, or no change in energy.
> Converged to machine precision,
> but not to the requested precision Fmax < 1
>
> Double precision normally gives you higher accuracy.
>
> writing lowest energy coordinates.
>
> Steepest Descents converged to machine precision in 190 steps,
> but did not reach the requested Fmax < 1.
> Potential Energy = -9.8216992e+02
> Maximum force = 2.7798114e+02 on atom 334
> Norm of force = 5.9967701e+01
> /////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
>
> editconf -f try2-vacuum.pdb -o try2-newbox.gro -bt dodecahedron -d 2.0
>
> (P.S I used the -d 4.0 once, just a bit crazy large to test it)
> /////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
>
> No velocities found
> system size : 4.567 2.350 1.422 (nm)
> diameter : 4.619 (nm)
> center : -0.010 -0.047 -0.232 (nm)
> box vectors : 0.000 0.000 0.000 (nm)
> box angles : 0.00 0.00 0.00 (degrees)
> box volume : 0.00 (nm^3)
> shift : 6.474 6.511 3.279 (nm)
> new center : 6.464 6.464 3.047 (nm)
> new box vectors : 8.619 8.619 8.619 (nm)
> new box angles : 60.00 60.00 90.00 (degrees)
> new box volume : 452.68 (nm^3)
> /////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
>
> genbox -cp try2-newbox.gro -cs spc216.gro -p topol.top -o try2-water.pdb
>
> ////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
> Containing 450 atoms in 52 residues
> Initialising van der waals distances...
> Reading solvent configuration
> "216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984"
> solvent configuration contains 648 atoms in 216 residues
>
> Initialising van der waals distances...
> Will generate new solvent configuration of 5x5x4 boxes
> Generating configuration
> Sorting configuration
> Found 1 molecule type:
> SOL ( 3 atoms): 21600 residues
> Calculating Overlap...
> box_margin = 0.315
> Removed 14442 atoms that were outside the box
> Neighborsearching with a cut-off of 0.48
> Table routines are used for coulomb: FALSE
> Table routines are used for vdw: FALSE
> Cut-off's: NS: 0.48 Coulomb: 0.48 LJ: 0.48
> System total charge: 0.000
> Grid: 21 x 21 x 15 cells
> Succesfully made neighbourlist
> nri = 89426, nrj = 2521641
> Checking Protein-Solvent overlap: tested 8637 pairs, removed 783 atoms.
> Checking Solvent-Solvent overlap: tested 474780 pairs, removed 5133 atoms.
> Added 14814 molecules
> Generated solvent containing 44442 atoms in 14814 residues
> Writing generated configuration to try2-water.pdb
> Protein
>
> Output configuration contains 44892 atoms in 14866 residues
> Volume : 452.675 (nm^3)
> Density : 999.711 (g/l)
> Number of SOL molecules: 14814
>
> Processing topology
> Adding line for 14814 solvent molecules to topology file (topol.top)
>
> //////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
>
>
> grompp -f minim.mdp -c try2-water.pdb -p topol.top -o try2-water.tpr
>
> genion -s try2-water.tpr -o try2-water-ions.pdb -conc 0.15 -neutral -pname NA+ -nname CL-
>
> /////////////////////////////////////////////////////////////////////////////////////////////////////////////////
> Reading file try2-water.tpr, VERSION 4.0.7 (single precision)
> Using a coulomb cut-off of 1 nm
> Will try to add 43 NA+ ions and 41 CL- ions.
>
> ///////////////////////////////////////////////////////////////////////////////////////////////////////////////////
>
> After vim the topol.top and the minim.mdp which pbc=no to pbc=xyz,
>
> grompp -f minim.mdp -c try2-water-ions.pdb -p topol.top -o try2-EM-water-ions.tpr
>
> ////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
> double-checking input for internal consistency...
> ERROR: One of the box lengths is smaller than twice the cut-off length. Increase the box size or decrease rlist.
> --------------------------------
> ///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
>
> but if I still used the pbc=no, it will work fine at this steps.
>
> Thanks and regards,
>
> lina
>
> ________________________________________
> From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on behalf of Dallas B. Warren [Dallas.Warren at pharm.monash.edu.au]
> Sent: Tuesday, June 15, 2010 11:15 AM
> To: Discussion list for GROMACS users
> Subject: RE: [gmx-users] the box lengths
>
> As already mentioned by Justin, unless you copy and paste the commands
> and output you got, for us to see, we can only have stabs in the dark
> (which is what I did since you are missing lots of information on what
> you are actually doing) to what is actually going on. And don't type in
> the commands into your email client, physically go and copy and paste
> the text in, otherwise you are filtering it through your own mind.
>
> Go and run the series of commands that work, copy / paste the results
> for us to see.
>
> Then go and run the series of commands that don't work, copy / paste
> again.
>
> Catch ya,
>
> Dr. Dallas Warren
> Drug Delivery, Disposition and Dynamics
> Monash Institute of Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3010
> dallas.warren at pharm.monash.edu.au
> +61 3 9903 9167
> ---------------------------------
> When the only tool you own is a hammer, every problem begins to resemble
> a nail.
>
>
>> -----Original Message-----
>> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-
>> bounces at gromacs.org] On Behalf Of #ZHAO LINA#
>> Sent: Tuesday, 15 June 2010 12:32 PM
>> To: Discussion list for GROMACS users
>> Subject: RE: [gmx-users] the box lengths
>>
>> I used the same commands trying another proteins, but no problems. So
>> it's not the reason about the commands I used.
>>
>> It did not contain the same number of molecules after genion when I
>> changed the box size. The pressure coupling was not on, and I did not
>> reach this steps. The problem I had just the steps I did the energy
>> minimization after ions (NA+ and CL-) added.
>>
>> Thanks and regards,
>>
>> lina
>> ________________________________________
>> From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on
>> behalf of Dallas B. Warren [Dallas.Warren at pharm.monash.edu.au]
>> Sent: Tuesday, June 15, 2010 6:48 AM
>> To: Discussion list for GROMACS users
>> Subject: RE: [gmx-users] the box lengths
>>
>> Please copy and paste in the commands you are using, and the output.
>>
>> I suspect you have made your box bigger, but it still contains the
> same
>> number of molecules and you still have pressure coupling on. So when
>> you
>> start the simulation, not surprising that the box compresses again and
>> goes under 2nm again.
>>
>> Catch ya,
>>
>> Dr. Dallas Warren
>> Drug Delivery, Disposition and Dynamics
>> Monash Institute of Pharmaceutical Sciences, Monash University
>> 381 Royal Parade, Parkville VIC 3010
>> dallas.warren at pharm.monash.edu.au
>> +61 3 9903 9167
>> ---------------------------------
>> When the only tool you own is a hammer, every problem begins to
>> resemble
>> a nail.
>>
>>
>> > -----Original Message-----
>> > From: gmx-users-bounces at gromacs.org [mailto:gmx-users-
>> > bounces at gromacs.org] On Behalf Of #ZHAO LINA#
>> > Sent: Tuesday, 15 June 2010 12:04 AM
>> > To: jalemkul at vt.edu; Discussion list for GROMACS users
>> > Subject: RE: [gmx-users] the box lengths
>> >
>> >
>> > ________________________________________
>> > From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org]
>> on
>> > behalf of Justin A. Lemkul [jalemkul at vt.edu]
>> > Sent: Monday, June 14, 2010 10:02 PM
>> > To: Gromacs Users' List
>> > Subject: Re: [gmx-users] the box lengths
>> >
>> > #ZHAO LINA# wrote:
>> > > _______________________________________
>> > > From: gmx-users-bounces at gromacs.org
> [gmx-users-bounces at gromacs.org]
>> > on behalf of Justin A. Lemkul [jalemkul at vt.edu]
>> > > Sent: Monday, June 14, 2010 9:33 PM
>> > > To: Discussion list for GROMACS users
>> > > Subject: Re: [gmx-users] the box lengths
>> > >
>> > > #ZHAO LINA# wrote:
>> > >> Hi,
>> > >>
>> > >> First time I meet this problem,
>> > >> ERROR: One of the box lengths is smaller than twice the cut-off
>> > length.
>> > >> Increase the box size or decrease rlist.
>> > >> I just followed the advice increase the box size, I tried twice
> in
>> > the
>> > >> editconf about the box size, actually this box is really large
>> > enough
>> > >> for the testing consideration, but still has the same problem.
>> > >>
>> > >
>> > > Well, what are your box vectors? If they are < 2 nm, you will get
>> > this error
>> > > because of the minimum image convention.
>> > >
>> > >
>> >
>>
> http://www.gromacs.org/Documentation/Terminology/Minimum_Image_Conventi
>> > on
>> > >
>> > > -Justin
>> > >
>> > > system size : 4.581 2.380 2.715 (nm)
>> > > diameter : 4.889 (nm)
>> > > center : -0.012 0.003 -0.904 (nm)
>> > > box vectors : 0.000 0.000 0.000 (nm)
>> > > box angles : 0.00 0.00 0.00 (degrees)
>> > > box volume : 0.00 (nm^3)
>> > > shift : 9.678 9.664 5.461 (nm)
>> > > new center : 9.667 9.667 4.557 (nm)
>> > > new box vectors : 12.889 12.889 12.889 (nm)
>> > > new box angles : 60.00 60.00 90.00 (degrees)
>> > > new box volume :1514.05 (nm^3)
>> > >
>> > > This one I set was really large, but still showed that problems.
>> > >
>> >
>> > What problems? The same error about the box lengths being shorter
>> than
>> > twice
>> > the cutoff? I don't think that's possible, given those vectors, if
>> > you're
>> > keeping your cutoffs at 1.0 nm.
>> >
>> > -Justin
>> >
>> > I do keep the cut-off. That's I do not know why. Four times had been
>> > tried.
>> >
>> > > Thanks,
>> > >
>> > > lina
>> > >
>> > >
>> > >
>> >
>> > --
>> > ========================================
>> >
>> > Justin A. Lemkul
>> > Ph.D. Candidate
>> > ICTAS Doctoral Scholar
>> > MILES-IGERT Trainee
>> > Department of Biochemistry
>> > Virginia Tech
>> > Blacksburg, VA
>> > jalemkul[at]vt.edu | (540) 231-9080
>> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>> >
>> > ========================================
>> > --
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--
Tsjerk A. Wassenaar, Ph.D.
post-doctoral researcher
Molecular Dynamics Group
Groningen Institute for Biomolecular Research and Biotechnology
University of Groningen
The Netherlands
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