ction run or analysis?
>
> Is it possible to re-center all molecules?
>
>
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
--
James "Wes" Barnett
Postdoctoral Research Scientist
Department of Chemical Engineering
Kumar Research Group <http://www.co
actions at 2^(1/6)*sigma and shift
the potential at the cutoff to zero in your table. If you want different
size spheres you need to subtract an additional term from r in the
denominators of the c6 and c12 terms.
--
James "Wes" Barnett
Postdoctoral Research Scientist
Department of Chemical
ot direction-periodic) you will
probably have to use a flat-bottom restraint to keep your solutes along the
z-axis.
--
James "Wes" Barnett
Postdoctoral Research Scientist
Department of Chemical Engineering
Kumar Research Group <http://www.columbia.edu/cu/kumargroup/>
Columbia Univers
he archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send
elds have obtained C6 and C12 values in their .itp files
> for each atom?
>
That depends on what the purpose of your simulation is. If you're just
wanting a Lennard-Jones fluid, sigma=1.0 and epsilon=1.0 in reduced units
could be reasonable.
>
>
> Best regards
>
>
> On Tue,
s provided by
mdrun to run multiple simulations at the same time with one mdrun command.
--
James "Wes" Barnett
Postdoctoral Research Scientist
Department of Chemical Engineering
Kumar Research Group <http://www.columbia.edu/cu/kumargroup/>
Columbia University
w.barn.
the charge is off.
>
> Looking for the some advice on how to proceed from here.
>
I do something like this:
vdw-lambdas = 0.00 0.00 0.00 0.00 0.00 0.10 0.20 0.30 0.40
0.50 0.60 0.70 0.80 0.90 1.00
coul-lambdas = 0.00 0.25 0.50 0.75 1.00 1.00 1.00 1.00 1.00
would even suggest upgrading to the latest release (2016.x series).
--
James "Wes" Barnett
Postdoctoral Research Scientist
Department of Chemical Engineering
Kumar Research Group <http://www.columbia.edu/cu/kumargroup/>
Columbia University
w.barn...@columbia.edu
http://wbarnett.us
--
Is that what you've done?
Justin's tutorial gives an explanation on why this needs to be done, and in
his topology he had all charges at 0.0 in the methane topology file.
--
James "Wes" Barnett
Postdoctoral Research Scientist
Department of Chemical Engineering
Kumar Research Group <h
ks in advance
> Surya
> Graduate student
> India.
>
Hard to know since we don't know what your system is or why you are using
position restraints and then removing them. Have you contacted the author
of the tutorial?
--
James "Wes" Barnett
Postdoctoral Research Scientist
Department
fferent combinations of MPI ranks and OMP
threads along with specifying the GPU's multiple times. I always do a
series of short runs with different combinations before choosing the
fastest one for a particular system and then doing a longer production run.
See http://www.gromacs.org/Docum
t; -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda
> -DCMAKE_INSTALL_PREFIX=/Bio/BioTools/gromacs
>
> I have not seen any errors during installation.
>
You should go ahead and just install 2016.3 instead of 5.1.
What is your exact command when you run mdrun?
--
James "Wes" Barnett
Po
t; Justin's tutorial gives an explanation on why this needs to be done, and
> >> in
> >> his topology he had all charges at 0.0 in the methane topology file.
> >>
> >>
> >> Okey, one thing that I presumed while performing the second
> >> transformation is t
so I have the impression that I get a mixture of the two versions !?
>
>
>
It looks like to me you also have 2016.1 installed and are calling that one.
You specified "/home/cloison/Softwares/GROMACS2016/gromacs-2016.3" as the
installation path for 2016.3, but gmx shows to be located at
ams ] actually seems like the right place, since I've read
> > that the parameters there *will* override the combination rules, but it
> > looks like this section doesn't take atom numbers, but only atom types.
> > Since I want these bonds to be based on site locations, this won't wor
take atom numbers, but only atom types.
> Since I want these bonds to be based on site locations, this won't work. Is
> there a way to specify non-bonded parameters using atom numbers?
>
> Any clarification you can provide will be helpful.
>
Before delving into this too much, to
ince the
methane molecule will have gone across the peridiodic boundary condition
several times.
I believe you need to use "gmx trjconv" with the "-pbc nojump" option. Then
you can run "gmx msd" on the new xtc file. See "man gmx-trjconv" for more
information on h
t;
Yes, see the options here:
http://manual.gromacs.org/documentation/2016.4/user-guide/mdp-options.html
--
James "Wes" Barnett
Postdoctoral Research Scientist
Department of Chemical Engineering
Kumar Research Group <http://www.columbia.edu/cu/kumargroup/>
Columbia University
w.barn...@colum
tput/write the C6 and C12 values generated by gromacs to
> screen/file.
>
gmx dump -s topol.tpr
That will give you the processed topology, which includes c6 and c12.
--
James "Wes" Barnett
Postdoctoral Research Scientist
Department of Chemical Engineering
Kumar Research Group &l
force field, and then calculating
and storing c6 and c12 in memory (8x8=64). I'm not sure what order it
processes things in though. Try doing some of the combining by hand and see
what matches up.
--
James "Wes" Barnett
Postdoctoral Research Scientist
Department of Chemical Engineering
Kumar
y handle dihedral
> restraints, and the pull code restraints
> How to apply angle/distance/position restraints with respect to lambda?
>
I don't believe those other restraints can be coupled for free energy
changes in GROMACS at this time.
--
James "Wes" Barnett
Postdoctoral Research S
o resolve it.
>
You went the wrong direction and increased the size of the time step,
unless that is a typo.
>
> Thanks in advance
> Surya
> Graduate student
> India.
>
--
James "Wes" Barnett
Postdoctoral Research Scientist
Department of Chemical Engineering
Kumar Resear
indicates you should try changing how neighbor searching is done.
Have you tried that?
--
James "Wes" Barnett
Postdoctoral Research Scientist
Department of Chemical Engineering
Kumar Research Group <http://www.columbia.edu/cu/kumargroup/>
Columbia University
w.barn...@columbia.
om decoupled state to real interactions.
>>
>>
Have you tried other FE estimate algorithms (i.e. thermodynamic
integration, MBAR, etc.). Look into the project "alchemical-analysis". It's
a python script that will give you some good visualizations on what is
happening at that last step
and what is the mathematical operation behind this
> operation
>
> any of you can help me?
>
Emiliano,
There is a paragraph in the GROMACS reference manual which cites a paper
which uses this method. I suggest starting with that paper and looking at
the background there and the references it cite
re attempting to
achieve, how you are trying to do so (perhaps including input scripts), and
what the exact problem is.
Wes
--
James "Wes" Barnett
Postdoctoral Research Scientist
Department of Chemical Engineering
Kumar Research Group <http://www.columbia.edu/cu/kumargroup/>
Columbia Uni
reating an index file using "gmx make_ndx" to create an index group
containing just the atoms you want. Then use "gmx trjconv" to output a file
only containing that group. See the "-h" flag for both of those commands.
--
James "Wes" Barnett
Postdoctora
>
>
> Could you guide me through a proper string definition in the mdp options to
> get separate files, in order to use the BAR algorithm afterwards?
>
> Best regards
>
> *Javier*
> --
> Gromacs Users mailing list
&g
28 matches
Mail list logo
