On 2010-07-01 11.19, Rolf Erwin Isele-Holder wrote:
Hi,
I used the GROMOS FF but changed the parameters (sigma, epsilon, charges, 1-4
interaction, combination rule for LJ, bond length strength, dihedrals, angles)
so that they are equal to the parameters used by the other authors with their
AMBER FF. The equations uses to calculate the energy are the same, that is why
I expected to get the same results. ...so I guess this assumption is not true.
Why is it not possible to use these parameters?
Is there a way to get a topology of glycerol working with gromacs instead of
writing it oneself? I've already tried the Prodrg Server but I didn't get
proper results with this topology, either.
in order to debug these things you need to compare energies at step
zero, preferably for one molecule first. IIRC amber does not use the
factor 1/2 in harmonic potentials, so you would have to multiply the
force constant by two.
Regards,
Rolf
On 07/01/10, Alan<alanwil...@gmail.com> wrote:
Hold on, you said *amber*, nevertheless you top has definitions for GROMOS**.
Either you are mixing force fields here (which *bad*) or worse, your not using
Amber FF, which is *really bad*.
I would be helpful if you give the commands you're using for pdb2gmx and
grompp. Besides, are you aware of ffamber and acpype? Since you said you have
the parameters for glycerol you may not need to build the topology anew, but I
do recommend looking at acpype.googlecode.com(http://acpype.googlecode.com) to
know more about simulations involving amber ff and gromacs, besides links to
important resources like ffamber.
Cheers,
Alan
On Thu, Jul 1, 2010 at
09:13,<gmx-users-requ...@gromacs.org<gmx-users-requ...@gromacs.org>> wrote:
Dear gromacs-users,
I've been simulating a box of liquid glycerol. The parameter's I have used were
taken from an article, whose authors achieved good agreement between their
simulation and experiments. These authors used an amber force field and the
software ORAC.
I used exactly the same parameters as them for my topology and very similar
settings in my mdp file. However I did not get the same results as them. Do you
know why I get these different results? I am in doubt weather the top of my
topology is correct, so I pasted it here:
#define _FF_GROMOS96
#define _FF_GROMOS53A6
[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 2 yes 0.5 0.8333
[ atomtypes ]
;name at.num mass charge ptype sigma epsilon
OA 8 0.000 0.000 A 0.3442 0.879228
C 6 0.000 0.000 A 0.3816 0.45803592
H 1 0.000 0.000 A 0 0
HC 1 0.000 0.000 A 0.2774 0.06573276
[ moleculetype ]
Glycerol 3
[ atoms ]
; nr type resnr resid atom cgnr charge
1 OA 1 GLCR OAA 1 -0.585 15.9994
2 H 1 GLCR HAA 1 0.396 1.008
3 C 1 GLCR CAD 1 0.182 12.011
.....
I think, that by specifying comb-rule = 2 giving sigma and epsilon is correct
instead of c6 and c12. The 0.5 for fudgeLJ and the 0.8333 for fudgeQQ are
supposed to lower the 1-4 interaction.
Regards,
Rolf
--
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
http://www.bio.cam.ac.uk/~awd28<<
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
sp...@xray.bmc.uu.se http://folding.bmc.uu.se
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