[gmx-users] size of the molecule

[raj vel]

hello all,
i am unable to do mdrun, for a protein with 504
aminoacids. while mdrun, LINCS warning and the
pressure coupling is more than 1 amu and this aborts
the mdrun. i was informed to increase tau_p, even that
is not working. 
but when i split the molecule (from PDB) into 100
aminoacid each, mdrun runs properly. but the time
taken by each fragment for mdrun differs very high.(
45 min for one segment and 48 hours for another
segment).

is that possible to do mdrun for a molecule with such
high no. of amino acids??
any suggestions
thanks in advance.

=====
ALAGURAJ.V
STRUCTURAL BIOLOGY LAB,
MADURAI KAMARAJ UNIVERSITY.

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