[gmx-users] Re: amber force field in Gromacs
servaas.michielssens at student.kuleuven.be
Tue Dec 1 09:52:13 CET 2009
> 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
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
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