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

[Jack Shultz]

Oh I see this tutorial solvates before minimization. I'm heading out,
but I'll give it a go tonight.

On Mon, Mar 9, 2009 at 3:57 PM, Jack Shultz <jshultz at hydrogenathome.org> wrote:
> 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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> http://hydrogenathome.org
>



-- 
Jack

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http://hydrogenathome.org