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

From: dbaogen (dbaogen_at_gmail.com)
Date: Tue Dec 10 2013 - 06:02:25 CST

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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