[gmx-users] Re: amber force field in Gromacs
servaas
servaas.michielssens at student.kuleuven.be
Tue Dec 1 11:18:00 CET 2009
> ------------------------------
>
> Message: 4
> Date: Tue, 01 Dec 2009 10:51:17 +0100
> From: Erik Marklund <erikm at xray.bmc.uu.se>
> Subject: Re: [gmx-users] Re: amber force field in Gromacs
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4B14E715.3030905 at xray.bmc.uu.se>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Hi,
>
> Vacuum simulations are trickier than in solvent, more often causing
> lincs errors. Have you tried playing around with lincs order and lincs iter?
>
> /Erik
Thanks for your suggestion, I tried without success and I also tried
shake. But this is also rather fighting the symptoms than the cause...
And amber simulations in vacuum do work fine... My personal guess was
that another parameter in my mdp file was not compatible with the amber
force field, but I could not figure out which one. I also tried
different settings, e.g. the one I found on the acpypi wiki.
>
> servaas skrev:
> >> Message: 6
> >> Date: Tue, 01 Dec 2009 07:38:29 +1100
> >> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> >> Subject: Re: [gmx-users] amber force field in Gromacs
> >> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> >> Message-ID: <4B142D45.5050909 at anu.edu.au>
> >> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> >>
> >> servaas wrote:
> >>
> >>> Hello,
> >>>
> >>> I tried using the amber force field in GROMACS. I proceeded as follows:
> >>> Determined my parameters with RED/ANTECHAMBER/tleap converted them with amb2gmx.pl
> >>> (or with acpypi, problem is the same) to gromacs coordinate and topology files. It concerns a modified nucleotide. I minimized with steepest descent, everything was fine.
> >>> When I tried running a simulation in single precision with this .mdp file (only nucleotide without solvent):
> >>>
> >>> integrator = md
> >>>
> >>> dt = 0.002
> >>> nsteps = 250000
> >>> nstcomm = 1
> >>>
> >>> ;output
> >>> nstxout = 1
> >>> nstvout = 1
> >>> nstfout = 0
> >>> nstlog = 500
> >>> nstenergy = 1
> >>>
> >>> nstlist = 10
> >>> ns_type = grid
> >>> rlist = 1.2
> >>> coulombtype = PME
> >>> rcoulomb = 1.2
> >>> vdwtype = cut-off
> >>> rvdw = 1.2
> >>>
> >>> fourierspacing = 0.12
> >>> pme_order = 4
> >>> ewald_rtol = 1e-5
> >>>
> >>> ;constraints
> >>> constraints = all-bonds
> >>>
> >>>
> >>> ; temperature coupling is on
> >>> Tcoupl = v-rescale
> >>> tau_t = 0.1
> >>> tc-grps = system
> >>> ref_t = 300
> >>>
> >>> pcoupl = no
> >>>
> >>> I get LINCS errors and eventually a crash. Now I tried running the same simulation with the same force field parameters in amber and everything was fine.
> >>> I also ran the calculation in GROMACS with double precision here again everything was fine... I also tried running a small nucleic acid fragment (so no modified parameters here)
> >>> that I created in tleap and converted to GROMACS again this crashes with lincs errors in GROMACS. When I look at the trajectories it is the O4' of the ribose who clashes with the O3'.
> >>>
> >>> The fact that I still get this problem with non modified amber parameters makes me thing there is something wrong with my .mdp file to run with amber FF, any suggestions?
> >>> Strange also that double precision seems to work just fine....
> >>>
> >> When switching precision, are the starting configurations different?
> >> What are the actual command lines in your procedures?
> >>
> > It is the exact same structure, when I look at the trajectory I see the
> > O3'-H rotate towards the O4' in the single precision trajectory they
> > come too close and clash. In the double precision trajectory the O3'-H
> > also rotates towards O4' but they do not come so close...
> >
> > I did not include the command lines for amber and RED, please let me
> > know if they are relevant to you.
> > So first I use RED to determine the charges of different fragments of my
> > molecule. The result are several mol2 files, I use tleap to combine this
> > mol2 file with parts of existing amber fragments. I save an amber top
> > and amber crd file. I convert this with amb2gmx or with acpypi (tried
> > both same result in the simulation).
> > ./amb2gmx.pl --prmtop ad_amber.top --crd ad_amber.crd --outname ad_gro
> > or
> > python acpypi.py -x ad_test.crd -p ad_test.top -o gmx -b gro
> > Then I add a box in gromacs:
> > editconf -bt dodecahedron -d 1.0 -f ad_amber.gro -o ad_box.gro
> > I run a minimization:
> > grompp -f md.mdp -c ad_box.gro -p ad_gro.top -o em.tpr
> > mdrun -deffnm em
> > (Also tried putting a position restraint step in between, did not
> > resolve the problem)
> > grompp -f md.mdp -c em.gro -p ad_gro.top -o md.tpr
> > mdrun -deffnm md
> >
> > Extra remarks: Simulation in vacuum is not realistic and the FF is not
> > made for this but I also tried running it with counter ions and water,
> > same result. In amber I can simulate the exact same molecule in vacuum,
> > with same parameters without any problems. The exact same problem occurs
> > if I start with a small natural nucleic acid sequence (3*DA), so 100%
> > amber FF parameters (but created in amber and converted with
> > amb2gmx.pl).
> >
> > Kind regards,
> >
> > Servaas
> >
> >
> >> Mark
> >>
> >>
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> >> End of gmx-users Digest, Vol 67, Issue 152
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> >>
> >
> >
>
>
> --
> -----------------------------------------------
> Erik Marklund, PhD student
> Laboratory of Molecular Biophysics,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596, 75124 Uppsala, Sweden
> phone: +46 18 471 4537 fax: +46 18 511 755
> erikm at xray.bmc.uu.se http://xray.bmc.uu.se/molbiophys
>
>
>
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