hi folks,
i'm a little stuck in the question whether the order of atom indices
(a1-a2-a3-a4 or a4-a3-a2-a1) plays any role when defining an
additional/new proper dihedral. as usual, i utilize the amber99sb force
field.
for the computation of the potential, the order shouldn't play any role,
there's also an executable topology merger available written in python
called gromacs_topology_merger.py as part of a the software package
ZIBMolPy designed for conformational analysis at
https://github.com/CMD-at-ZIB/ZIBMolPy
given (in the same directory) a topology file topol.top (argument
that is checked apart from gbsa.itp?!
thanks again,
vedat
Am 04.05.2012 11:23, schrieb Alan:
Hi there,
look at 'acpype -h', in particular:
-g, --disambiguatedisambiguate lower and uppercase atomtypes in
GMX top
file
Alan
On 3 May 2012 14:34, Vedat Durmaz dur
.
any idea what might cause that?
Am 04.05.2012 15:26, schrieb Justin A. Lemkul:
On 5/4/12 9:14 AM, Vedat Durmaz wrote:
thanks justin and alan.
i also had the suspicion that the error is caused by case
sensitivity. simply
replacing all atom types from lower to upper case within
in /Complex.top/.
Are you inserting your gbsa.itp in the *right* place of your top file?
Alan
On 4 May 2012 14:14, Vedat Durmaz dur...@zib.de
mailto:dur...@zib.de wrote:
thanks justin and alan.
i also had the suspicion that the error is caused by case
sensitivity. simply replacing all
parameter values)
to add GAFF atom types like e.g. ss, hn, hx, os to the gbsa.itp
file?
thanks in advance and take care
vedat durmaz
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hi francesca,
i think what you are looking for is this
g_sgangle $indexFile -f $traj -s $tpr -oa $outfile
before that, you have to define two planes (by 3 atom indices each) in
your index file
[ dihed1 ]
523 680 3482
[ dihed2 ]
680 3482 3691
which you choose when having started
i always did it (successfully) with one single command:
trjconv -f md.trr -s md.tpr -o mdCompact.trr -pbc mol -ur compact -n
../../index.ndx
regards
vedat
Am 29.02.2012 18:01, schrieb Steven Neumann:
Dear Gmx Users,
I am run a simulation with Gromacs 4.5.4. of my protein and 15
ligands.
hi steven,
i've been simulating a 33 AA peptide for the past two days using
implicent solvent in order to achieve a proper folding.
i haven't added counterions, however, the systems shows nice results
according to what i've expected. the mdrun command (for the extension)
for our hardware
, 2012 at 12:14 PM, Vedat Durmaz
dur...@zib.de mailto:dur...@zib.de wrote:
hi steven,
i've been simulating a 33 AA peptide for the past two
days using implicent
solvent in order to achieve a proper folding.
i
thanks justin for clearing up these issues ..
Am 28.02.2012 15:50, schrieb Justin A. Lemkul:
Vedat Durmaz wrote:
actually, as far as i know, the -DFLEXIBLE argument has no effect
on simulations without explicit water ?!
The #ifdef FLEXIBLE block does only affect explicit water
Lambda
0 0.0 0.0
Steepest Descents converged to Fmax 1000 in 1 steps
Potential Energy = inf
Maximum force = 0.000e+00 on atom 0
Norm of force = nan
Can you please explain?
Steven
On Tue, Feb 28, 2012 at 2:29 PM, Vedat Durmaz dur...@zib.de
mailto:dur...@zib.de wrote
hi guys,
i have a molecular system that i want to simulate many times with
differing initial conditions, but each with the same number of (solvent)
atoms! i'm using gromacs 4.5.4 ...
genbox with -cs gives me different numbers of solvent molecules.
putting more than 20,000 tip4p molecules
thanks to you two, mark justin! that's it ...
-maxsol was the keyword for this problem. (which i actually could have
found it myself if having looked carefully after typing genbox -h)
Am 09.01.2012 13:57, schrieb Mark Abraham:
On 9/01/2012 11:24 PM, Vedat Durmaz wrote:
Am 09.01.2012 12
thanks mark. i guess it took some time answering all these questions.
and i think you are right. trying to interpret each computed energy term
seperately in a physical manner is senseless. especially since i'm not
really deep inside the force field implementation stuff. however, with
one of
Am 20.10.2011 15:01, schrieb Mark Abraham:
On 20/10/2011 7:25 PM, Vedat Durmaz wrote:
thanks mark. i guess it took some time answering all these questions.
and i think you are right. trying to interpret each computed energy
term seperately in a physical manner is senseless. especially since
the simulation and on which
energy terms to concentrate in order to get reliable results?
thanks in advance and sorry for the long text ... as i've already told
you, i'm really confused.
kind regards
vedat durmaz
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hi alan and all others,
i love it. i've probably never seen such a helpful and constuctive
answer to a question asked over the gmx user mailing list. following
your instructions was very informative on the one hand and provided the
results that i needed on the other.
slightly modifying the the
Alan schrieb:
Dear Vedat,
On Wed, May 19, 2010 at 20:36, gmx-users-requ...@gromacs.org
mailto:gmx-users-requ...@gromacs.org wrote:
@rui
acpypi -i ch3cn_210.pdb
says: cannot find template for residue C3N in our library. and
indeed,
there's no residue C3N in my
hi all together,
this week i'm trying to do some simulations with acetonitrile (AN) as a
solvent and using ffamber99 as force field. on this website
http://www.pharmacy.manchester.ac.uk/bryce/amber#box
i found a gorgeous little box containing a pretty number of 6-site
modeled AN molecules,
hello out there,
i'm trying to simulate a receptor ligand system in order to extract
intermolecular non-bonded interaction energies (vdw/coulomb) and apply
the linear interaction energy model.
which parameter settings do you recommend for highly accurate results?
up to now, i had chosen (copied
Mark Abraham schrieb:
On 31/03/2010 11:44 PM, vedat durmaz wrote:
thanks to both of you for your helpful hints. actually, i'm not using
the LIE method as available with the gromacs package, but planning to
implement the model myself using energies from gromacs runs.
Sure... it's still only
dear gromacsters,
does anyone know a way to tell gromacs which molecule's coordinates to
write to the output file which should be as small as possible? i don't
need the solvent's coordinates for example.
starting run like:
grompp -f ../../md.mdp -c eq.gro -n index.ndx -p complex.top -o md.tpr
hi out there,
still doing my first steps on the gmx planet. can anyone tell me, why
there are 3 columns in the output file of g_hbond and how to interpret
the output values when having run
g_hbond -f mdNew.xtc -s md.tpr -num mdNew_numH.xvg
first column frame!
second column = #H bonds?
third
thanks. things are getting clearer and life's going a little easier, now.
Justin A. Lemkul schrieb:
dur...@zib.de wrote:
hi there,
it's my first steps with gromacs and i can't get rid of the following
problem:
i set up my box with
editconf -bt dodecahedron -f complex.pdb -o
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