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

From: dbaogen (dbaogen_at_gmail.com)
Date: Thu Dec 12 2013 - 19:02:30 CST

Hi,
  
     Thanks for your suggestion. Using SMD in NAMD software, if we impose harmonic restriction on the center of alpha carbons of protein, the ligand can be pulled out. But I am not sure whether this will introduce artificial effect on the simulated system. Would you like to give me some suggestions about the simulation. Thanks.

Best
Duan Baogen


From: Norman Geist
Date: 2013-12-10 22:18
To: 'dbaogen'
CC: Namd Mailing List
Subject: AW: namd-l: puzzle of SMD in NAMD-2.9 and pull code in Gromacs
Hi,
I dont think that this is a problem of the implementatio of the pulling. Its 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: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] 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!
 
Best
 
Duan Baogen




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