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 calculated and the
program crashes.
But I am not sure that was your problem. You mentioned that the
program was
stopping due to too many lincs warnings. Cycles (trp, phe, his) seemed
to be the
cause.
Do you still have lincs warnings, may be less?
The other thing is that is your protein deforms as much as before,
there is another
way to simulate you protein with Martini:
http://md.chem.rug.nl/cgmartini/index.php/tools/118-end
XAvier.
On Apr 20, 2010, at 7:16 AM, Trang wrote:
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 19, 2010 at 4:26 PM, Martti Louhivuori <m.j.louhivu...@rug.nl
> wrote:
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 dihedrals, especially if
running with a larger timestep (30fs).
Here is the system topology.
----------------------------
#include "../martini_v2.1.itp"
#include "../martini_v2.1_aminoacids.itp"
The last line is unnecessary. Use it only when simulating single
aminoacids instead of a polypeptide.
Minimized structure showed no close contact (with distance cutoff
1.6, even to 1.9). Production run stopped at
That's only 0.16-0.19nm, so overlap is still possible.
step 175552 (5266.56 ps) with Segmentation fault, preceeded with a
lot of Lincs warnings (I set ring_bonds = "constraints"). This is
the mdp file, this file goes along with the system in vaccuum that
crashed. I'm not sure if
What's different this time around? Last time you said you couldn't
run it even in vacuum.
Sounds like you are just hitting statistical limits with your
combination of (extended) dihedrals + 30fs timestep. Use a smaller
timestep (20fs for example) or switch to local elastic bonds for the
beta-strands... and solvate the system (without overlap) so the
simulation makes some sense!
-martti-
--
Post-doctoral research fellow
Moleculaire Dynamica
University of Groningen
Nijenborgh 4, 9747AG Groningen, the Netherlands
tel. +(31) 50 363 4339 | fax. +(31) 50 363 4398
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