Il 16/03/2012 01:38, Mark Abraham ha scritto:
On 16/03/2012 6:02 AM, Francesco Oteri wrote:
Dear gromacs users,
I am trying to simulate a protein (containing FeS cluster and a
complex metal active site) using virtual site.
I've to face a problem with LINCS. In particular, if I constrain only
h-bonds without using virtual site,
simulation runs fine but constraining "all-bonds", simulation crashes
after a lot of LINCS warning like:
Step 356, time 0.712 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.408533, max 8.159325 (between atoms 2750 and 2754)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
2750 2754 90.0 0.1365 1.2502 0.1365
In both cases simulation conditions are the same. The bonds causing
problem belongs to the active site.
I am wondering if there are structural features imparing the use of
all-bonds constraints in LINCS.
A second question is, how can I run MD with virtual site without
all-bonds options.
Coupled constraints, such as you might have in a cluster, can be
delicate. Equilibrating with a quite small time step can be necessary.
Mark
Hi Mark,
I've run 100ps at 0.5fs, and 1fs...but when I switch to 2fs it crashes.
I've read in the manual and it seem that triangular structures might
introduce problem, but I dont have such a structure in my protein.
So, there are other coupled constraint that may cause problem in LINCS?
Is it possible that the force constants can cause problem?
Or anyway, is it possible using virtual site constraining only h-bonds?
Francesco
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