The representation of extended regions (b-sheets) is more stable using
elastic
bonds than a dihedral angle because the flexibility of the force field
makes possible
the occurrence of situations where the two bonds get aligned and
therefore the
plan used to defined the dihedral can not be
Hi,
the rmsd you show is for the protein in vacuum? It goes up to 0.7 nm!
That is a very
large deformation, is it expected? Isn't your protein freezing and all
the kinetic energy
going into translational motion.
there is a few things you could try.
1- First you should increase the rlilst
On 19 Apr 2010, at 06:49, Trang wrote:
The protein topo is too large, so I put it here. http://pastie.org/926617
The protein topology is fine, but you could try also with elastic
bonds instead of dihedrals in the extended regions (--elastic option).
Elastic bonds are more robust than
On Mon, Apr 19, 2010 at 4:08 PM, XAvier Periole x.peri...@rug.nl wrote:
Hi,
the rmsd you show is for the protein in vacuum? It goes up to 0.7 nm! That
is a very
large deformation, is it expected? Isn't your protein freezing and all the
kinetic energy
going into translational motion.
Elastic bonds did help the system survive. I'm not really understand why do
we need more robust bonds in this system. Does it mean that there exists
large forces that cause my system to blow up? Would you mind giving an
explanation?
Thanks indeed for your taking time to help.
Trang
On Mon, Apr
On Fri, Apr 16, 2010 at 5:17 PM, Martti Louhivuori m.j.louhivu...@rug.nlwrote:
On 15 Apr 2010, at 18:06, Trang wrote:
My target system is a protein with lipid molecules added randomly (using
GENBOX). Running MD, I expect to
I hope you're using a larger van der Waals distance (0.24nm or so)
On 15 Apr 2010, at 18:06, Trang wrote:
My target system is a protein with lipid molecules added randomly
(using GENBOX). Running MD, I expect to
I hope you're using a larger van der Waals distance (0.24nm or so)
when inserting the lipids.
broke down the problem, that is, to run md
Dear gmx users,
I'm trying to run some CG-MD with gromacs, using the available Martini FF.
The first run with {lipid + water} is fine. The POPC lipid bilayer is
successfully self-assembled. I then applied Martini FF for system involving
protein.
All the systems I've tried so far could not survive
It is mot likely that your preparation of the system is somehow
corrupted.
The insertion of a protein in a lipid bilayer might easily introduce
strong
forces in the system and thereby result in a crash of your simulation.
It is also possible that your protein topology is not describing
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