Hi Johnny,
I am not familiar with pulling and even less with gromacs but I would be
very cautious in using the MARTINI force field for the kind of
simulation
you are doing.
This CG model has not been tested at all for this and it might not be
very good at it! But I would be very interested
Hi Xavier (and Johnny),
I quite agree with what Xavier says. Still I would like to point out
that we have used CG models to pull on them and at least qualitatively
they behave quite reasonably, although these models have never been
parameterized or systematically tested with this kind of
Marc Baaden wrote:
Hi Xavier (and Johnny),
I quite agree with what Xavier says. Still I would like to point out
that we have used CG models to pull on them and at least qualitatively
they behave quite reasonably, although these models have never been
parameterized or systematically tested with
On Jul 30, 2009, at 11:40 AM, David van der Spoel wrote:
Marc Baaden wrote:
Hi Xavier (and Johnny),
I quite agree with what Xavier says. Still I would like to point out
that we have used CG models to pull on them and at least
qualitatively
they behave quite reasonably, although these
XAvier Periole wrote:
On Jul 30, 2009, at 11:40 AM, David van der Spoel wrote:
Marc Baaden wrote:
Hi Xavier (and Johnny),
I quite agree with what Xavier says. Still I would like to point out
that we have used CG models to pull on them and at least qualitatively
they behave quite reasonably,
On Jul 30, 2009, at 12:10 PM, David van der Spoel wrote:
XAvier Periole wrote:
On Jul 30, 2009, at 11:40 AM, David van der Spoel wrote:
Marc Baaden wrote:
Hi Xavier (and Johnny),
I quite agree with what Xavier says. Still I would like to point
out
that we have used CG models to pull on
Hi,
Just picking up the following bits of the conversation:
David van der Spoel wrote:
What does this boil down to? If you want to apply MD tools to get
an accurate force curve *now*, use all atom models. [..]
x.peri...@rug.nl said:
This is of course the idea, but then comes the problem of
Hi XAvier, Marc, and David,
Thank you so much for the reply and encouragement ;-). Please forgive me
as I am trying to learn how to reply to the thread that I started. With
regards to the fun discussion, it was my original intent to compare the
results of pulling with the MARTINI forcefield (if
Dear gromacs users,
Hi, I am trying to pull apart a relatively large protein (CG using the
martini force field) by pulling on two groups in opposite directions. To
do this, I will be using the following .mdp file. However, I am almost
certain that it contains errors:
title=
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