From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Fri Feb 26 2016 - 01:57:15 CST
Von: giulia palermo [mailto:giulia.palermo83_at_gmail.com]
Gesendet: Donnerstag, 25. Februar 2016 18:10
An: Norman Geist <norman.geist_at_uni-greifswald.de>
Betreff: Re: namd-l: problem in running targeted MD
thank you for your reply. I found the problem, it was in the restart file. Now the simulation is runnig. However, I have some other questions that you can clarify to me.
Nice, I’ll try, altough I’ve never used TMD.
1. By using VMD, I have calculated an RMSD initial of 7 Ang. I have used this value as TMDInitialRMSD. However, can the code guess this number by himself?
Moreover, when restarting the simulation, I assume that I will have to include in the input file the last value of the RMSD produced by the simulation. Is it correct or the code will take this value from the restart?
You do not need to initially specify this value, as pointed out by the manual, the default is computed from coordinates. BUT as I understood to have a continuing linear targeting bias, continuing namd runs should be
given the exact “same” value as the initial run AND given the firsttimestep (which is usually only needed for timestep numbering purpose) as last step (when restart file was written) so that NAMD can continue the steering without jumps.
2. My target PDB structure looks like that (below). As you see, I have specified 200 in the occupancy column for all the heavy atoms of the system.
This is because I want the these atoms to be dragged during the simualtion with a force constant of 200 kcal/mol/A^2. These atoms will be biased.
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