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
servaas skrev:
Message: 6
Date: Tue, 01 Dec 2009 07:38:29 +1100
From: Mark Abraham <mark.abra...@anu.edu.au>
Subject: Re: [gmx-users] amber force field in Gromacs
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID: <4b142d45.5050...@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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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
er...@xray.bmc.uu.se http://xray.bmc.uu.se/molbiophys
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