I would like to add that maybe the bins store Frame numbers. Because I seem
to have around 21000 frames and I guess I am unable to see a number higher
than that. Apologies for the confusion about earlier number. So, in this
case if I want a confirmation at a particular frame number, how should I
Justin,
so that means delete these lines
ATOM 7882 SOD UNK 1 42.69 -261.86 64.056 1.00 0.00 UNK
ATOM 7883 SOD UNK 1 39.09 -260.89 62.8968 1.00 0.00 UNK
ATOM 7884 SOD UNK 1 40.1388 -263.52 64.6776 1.00 0.00 UNK
ATOM 7885 SOD UNK 1
Dear Gmx Users,
I have my carbon nanotube (lenght z axis) with proteins attached to it. I
wish to collect RDF of given type of amino acids away from the surface in
two dimensions (xy). Z axis does not interest me. That would make a circle
then. My question: how to make a specific index group of
Thank you all for your comments! It's interesting that Patrick ran into the
same issues just a few days earlier.
Following your suggestions, I started some simulations with the
Reaction-Field-nec coulombtype. So far those have run for only about 30
nanoseconds, but based on the attached graph
Dear Gmx Users,
I have built a coarse grained force field from scratch for my specific
protein. I wish to increase the time step, to see how much I can push it.
How can I assess it to see whether I did not go over given value as its
sure system specific. Would advise of some properties? Its a
On Wed, Dec 18, 2013 at 6:58 AM, Lutz Maibaum lutz.maib...@gmail.comwrote:
Thank you all for your comments! It's interesting that Patrick ran into
the same issues just a few days earlier.
Following your suggestions, I started some simulations with the
Reaction-Field-nec coulombtype. So far
Note that Parrinello-Rahman contains some very minor approximations
(virial and kinetic energies off by 1/2 a step) that might affect
things by 0.3 atm. But that is almost certainly not the limiting
factor in the accuracy of the simulation.
On Mon, Dec 16, 2013 at 3:09 PM, Justin Lemkul
On Dec 17, 2013, at 1:55 PM, Mark Abraham mark.j.abra...@gmail.com wrote:
I would suggest using mdrun -rerun magic-configuration.gro -s some.tpr on
whatever combinations of .mdp settings and GROMACS versions make sense, to
observe that there is a difference that can be reproduced, and which
On 12/17/13 1:55 PM, jkrie...@mrc-lmb.cam.ac.uk wrote:
I think g_select does something like this. I am trying to do something
similar: make a selection of water within 5A or so of a residue in my
protein. Also need help please.
The examples at the end of g_select -select 'help all' pretty
