Hi Gromacs Users,
Pressure coupling is not supposed to scale the coordinates of my frozen
group, yet it is. My frozen group is a crystal structure that does not have
any topology assigned to them: no bond, angle, dihedral constants etc.
specified. I find that a crystal structure gets compressed.
Hello Gromacs Users,
I just wanted to share with you a simple fortran program I wrote that reads
a .xyz file and outputs a .pdb file. I'm sure some of you will find it
useful.
Chris Rowan
***
* This program reads a .xyz file and prints out
Here are some more details:
My cg minimized structure has a distance of 0.3 Angstroms between Ag
and another atom of another molecule.
Changing all my Ag to hydrogens and running a cg still gives a
distance of 0.3 Angstroms.
I could also add that each Ag belongs to its own charge group, so they
s
Hi Chris,
I've done a gmxdump and there aren't any zeros for any of the LJ values.
No capital letter problems either.
Chris Rowan
Mon, 27 Jul 2009 12:30:54 -0700
Sounds like your topology/forcefield is incorrect or incomplete.
Does your log file from mdrun or the stderr/stdout from grompp/md
Hello,
I'm using ffoplsaa with a new atom type (Ag) that I've included in the .atp
file, LJ parameters I've specified in the nb file. My system topology I've
written by hand in an itp file. The problem is that after any kind of run
the molecule penetrates the metal surface! This shouldn't be ha
Thanks for the response Justin.
"First, it would be helpful to know which version of Gromacs you're
using, especially if this is a bug in an older version. If it is the
most current version (4.0.5), it is of much greater interest :)"
I had been using version 3.3.2.
"What I don't understand is wh
Sorry to post again,
But I meant to say that for atom indexing I looked using gmxdump:
gmxdump_s -s ???.tpr -f ???.pdb -nr
and found only indexing starting at zero; e.g
atom[0]={name="AG"}
Cheers,
Chris Rowan
University of Victoria
2009/6/23 Christopher Rowan :
> Hi,
>
Hi,
Allow me to be the first to archive a message with "negative index".
I ask for an index file:
make_ndx_s -f ???.pdb -o ???.ndx
and specify:
a AG
to select all the silver atoms into a group.
The index file then clearly numbers and lists the atoms: all in [
system ], again all atom numbers in e
Hi,
I read that some have been using GROMACS to model epoxy polymers, and I'm
wondering which force field you've been using. I'd ideally like to
implement the new DFTB+ code into GROMACS to run some QM/MM simulations of
epoxy/TiO2 nanocomposites.
Thanks,
Chris Rowan
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