[gmx-users] size of the molecule
rajgrmx at yahoo.co.in
Thu Jul 22 12:15:45 CEST 2004
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
is that possible to do mdrun for a molecule with such
high no. of amino acids??
thanks in advance.
STRUCTURAL BIOLOGY LAB,
MADURAI KAMARAJ UNIVERSITY.
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