AW: puzzle of SMD in NAMD-2.9 and pull code in Gromacs

From: Norman Geist (
Date: Tue Dec 10 2013 - 08:18:03 CST


I don't think that this is a problem of the implementatio of the pulling.
It's more likely a stronger interaction between your protein and the ligand
than in the publication you found. Maybe you could give the proteins center
of mass a counter force.

Norman Geist.


Von: [] Im Auftrag
von dbaogen
Gesendet: Dienstag, 10. Dezember 2013 13:02
An: namd-l
Betreff: namd-l: puzzle of SMD in NAMD-2.9 and pull code in Gromacs


Dear all,


            Recently, I have a problem in using SMD to pull a ligand out
from the protein active site. In the course of pulling, the protein is
moving along with ligand. So the results are not consistent with our
expectation. If we impose the harmonic restraint on protein, the ligand can
be pulled out. But the artificial effect would be introduced if we did it
like that. Would anyone like to give me some suggestions about the SMD
simulation in NAMD?


          In addition, it is found that the pull code in Gromacs can also do
the SMD simulation. From the published results using pull code in Gromacs,
the protein itself was not restricted while pulling a ligand out from the
protien's active site. Would you like to explain the difference between SMD
in NAMD and pull code in Gromacs? Thanks in advance!




Duan Baogen

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