[gmx-users] Re: gmx-users Digest, Vol 59, Issue 58

[Jack Shultz]

Yes I read somewhere that treating the simulation space as a cube has
some drawbacks. I'll try these parameters.

On Mon, Mar 9, 2009 at 3:36 PM, Andrew Voronkov <drugdesign at yandex.ru> wrote:
> I've used this tutorial:
> https://extras.csc.fi/chem/courses/gmx2007/tutorial1/tutorial1.pdf
>
> I've used command line:  editconf -c -f conf.gro -bt dodecahedron -d 0.7 -o box.gro to center the protein, but the problem remains - protein is still in the edge of the water box.
>
> There is also 1-4 warning for which I see no reasons and very fast presision reached time.
>
> Steepest Descents:
>   Tolerance (Fmax)   =  1.00000e+01
>   Number of steps    =          200
> Warning: 1-4 interaction between 2 and 21 at distance 6.197 which is larger than the 1-4 table size 2.000 nm
> These are ignored for the rest of the simulation
> This usually means your system is exploding,
> if not, you should increase table-extension in your mdp file
> or with user tables increase the table size
> Step=   14, Dmax= 1.2e-06 nm, Epot=  2.82932e+24 Fmax=         inf, atom= 4
> Stepsize too small, or no change in energy.
> Converged to machine precision,
> but not to the requested precision Fmax < 10
>
> Double precision normally gives you higher accuracy.
> You might need to increase your constraint accuracy, or turn
> off constraints alltogether (set constraints = none in mdp file)
>
> writing lowest energy coordinates.
>
> Steepest Descents converged to machine precision in 15 steps,
> but did not reach the requested Fmax < 10.
> Potential Energy  =  2.8293175e+24
> Maximum force     =            inf on atom 4
> Norm of force     =            inf
>
> gcq#239: "killing children ..." (Insight/Parasoft)
>
> andrew at linux-f29d:~/GROMACS_MD/FZD1>
>
> Here are MDP files:
>
> EM.mdp
> integrator = steep
> nsteps = 200
> nstlist = 10
> rlist = 1.0
> coulombtype = pme
> rcoulomb = 1.0
> vdw-type = cut-off
> rvdw = 1.0
> nstenergy = 10
> constraints = none
>
>
> integrator = md
> nsteps = 2500
> dt = 0.002
> nstlist = 10
> rlist = 1.0
> coulombtype = pme
> rcoulomb = 1.0
> vdw-type = cut-off
> rvdw = 1.0
> tcoupl = Berendsen
> tc-grps = protein non-protein
> tau-t = 0.1 0.1
> ref-t = 298 298
> Pcoupl = Berendsen
> tau-p = 1.0
> compressibility = 5e-5 5e-5 5e-5 0 0 0
> ref-p = 1.0
> nstenergy = 100
> define = -DPOSRES
>
> Best regards,
> Andrew
>> ------------------------------
>> Message: 3
>> Date: Fri, 06 Mar 2009 13:41:28 -0500
>> From: "Justin A. Lemkul" <jalemkul at vt.edu>
>> Subject: Re: [gmx-users] .gro files problems
>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> Message-ID: <49B16E58.3000401 at vt.edu>
>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>> Andrew Voronkov wrote:
>> > Dear GROMACS users,
>> > I'm trying to do this tutorial
>> >
>> It's always best to post a link to the tutorial you're using.  There are dozens
>> of Gromacs tutorials out there.
>> > with 1ijy structure from rcsb.org
>> > All .gro files on different step raise questions.
>> > 1) conf.gro - by VMD I see some strange groups which are not linked with the protein.
>> This may or may not be an artefact of VMD's efforts to guess where bonds should
>> be.  Sometimes it's smart, sometimes it's not.
>> > 2) After solvatation step in solvated.gro the protein is not in the middle of solution but somewhere in the edge, how to solve this?
>> editconf -c
>> > 3) After energy minimization protein even goes out of the solution. Looks like I am doing everything according to the tutorial (except the structure) but there are still problems...
>> >
>> Use editconf -c and try again.
>> > The .gro files are in the attachment.
>> The listserv ate them, but they probably won't aid much in diagnosis, anyway.
>> > On minimization step I also get:
>> > Steepest Descents converged to machine precision in 73 steps,
>> > but did not reach the requested Fmax
>> Depending on what your target Fmax was, this may not be a problem.  Fmax < 1000
>> is generally adequate for a simple protein in water.
>> > On equilibration step I also get an error(with such .gro file it very proabable):
>> >
>> Or you could have an error in your .mdp file (inappropriate parameters, etc), so
>> if things continue to fail, post the .mdp file (not as an attachment, just embed
>> the text).
>> -Justin
>
>
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-- 
Jack

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