[gmx-users] the box lengths
#ZHAO LINA#
ZHAO0139 at e.ntu.edu.sg
Tue Jun 15 06:12:35 CEST 2010
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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