Dear Rahul,
On Tue, Jun 2, 2015 at 1:08 PM, Rahul verma rv010...@gmail.com wrote:
Dear Gmx Users,
I obtained topology files for fullerene from ATB website in order to
simulate
water confined in fullerene.However on energy minimization the fullerene
undergoes
complete structural
Dear Alexander,
As Vitaly has already suggested, it is possible to simulate growth.
I'd, on the other hand, underline what Micholas has said.
It may take some planning. Here are a few ideas how to do it.
1. If you are simulating cleaving/forming bonds, the topology would change
which is
Dear Bin,
On Sat, Aug 2, 2014 at 12:44 PM, massimo sandal deviceran...@gmail.com wrote:
Compile them with different suffixes? So that you have binaries like
mdrun_46 and mdrun_50 ?
Additional tip: if you don't want to rename all the executables
you may simply create a soft link to one of the
On Mon, Aug 4, 2014 at 7:08 AM, Tamas Karpati tkarp...@gmail.com wrote:
Dear Bin,
On Sat, Aug 2, 2014 at 12:44 PM, massimo sandal deviceran...@gmail.com
wrote:
Compile them with different suffixes? So that you have binaries like
mdrun_46 and mdrun_50 ?
Additional tip: if you don't want
Dear Justin,
I'm in the experimenting with [exclusions] for [thole_polarization].
Still not there but approaching... I'd like to ask more help as the
Manual is not detailed enough for me to comprehend the whole.
When using the core/shell model I expect the following extra
effects and functions
Dear Justin,
1. With a q_D charge on D, the normal q_A becomes q_C=q_A-q_D
to preserve the q_A=q_C+q_D atomic charge in a c/s simulation
(since D is attached to A). I assume that GROMPP expects q_C for
atoms, q_D for shell particles in the GRO files. Is this correct?
No. Every atom in
Dear Justin,
No, they're not mutually exclusive. The Thole function screens nearby
dipoles so they don't experience artificial forces. The
thole_polarization name is a bit unfortunate; it should really be
thole_screening instead.
I was probably confused by the two contribs in the MDRUN log
with a 1 nm radius for inclusion
while ca. 15000 for a radius of 0.5 nm.)
The total potential is almost a pure Coulombic one and is too large.
Do you have any hint on what could go wrong?
Thanks for your attention.
With best regards,
toma
On Fri, Jul 25, 2014 at 9:31 PM, Tamas Karpati tkarp
Dear all,
I have two questions about geometry optimization of a crystal
with polarization via the core/shell model. I'm creating *.gro and
*.top files by hand and compile them with *.mdp to *.tpr via
GROMPP. My FF is also made by hand (simply because i need
to learn GROMACS). I have learnt on
= no ; used to switch cell-optimization on/off
Best regards,
toma
On Fri, Jul 25, 2014 at 1:48 PM, Justin Lemkul jalem...@vt.edu wrote:
On 7/25/14, 7:43 AM, Tamas Karpati wrote:
Dear all,
I have two questions about geometry optimization of a crystal
with polarization via the core/shell model. I'm
Dear Justin,
Does your topology specify the proper intramolecular exclusions? What
is(are) the molecule(s)?
No bonds, no exclusions. The whole crystal is modelled by ions
interacting via forces of the Coulomb and Buckingham types.
In fact, there is an X-Y-X angle force type which does have an
Dear Justin,
Thanks for your educational answers.
Coulombic interactions fail at short distances; you probably need to apply
I was afraid of that... somehow removing shells from the cores in the
initial structure have let it functionally work (with not yet
reasonable results).
Thole
limit?
Once again, thank you very much -your answer saved me valuable time.
With regards,
toma
On Tue, Jul 8, 2014 at 9:50 AM, Mark Abraham mark.j.abra...@gmail.com wrote:
On Mon, Jul 7, 2014 at 3:17 PM, Tamas Karpati tkarp...@gmail.com wrote:
Dear all,
I have trouble creating a FF without
Dear all,
I have trouble creating a FF without bonds explicitely defined,
only using nonbonding forces of the Buckingham (BH) type to keep
my crystal in one piece. The problem is related to wrong interatomic
forces on basis of the ASCII-dumped TRR files. So FF works (at
least functionally),
14 matches
Mail list logo
