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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