[gmx-users] Re: amber force field in Gromacs
erikm at xray.bmc.uu.se
Tue Dec 1 10:51:17 CET 2009
Vacuum simulations are trickier than in solvent, more often causing
lincs errors. Have you tried playing around with lincs order and lincs iter?
>> 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:
>>> 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
>>> 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 = 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
> 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
> Kind regards,
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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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