AW: problem in running targeted MD

From: Norman Geist (
Date: Mon Feb 29 2016 - 01:37:21 CST


Yes, that sounds reasonable.


Norman Geist


Von: giulia palermo []
Gesendet: Samstag, 27. Februar 2016 01:37
An: Norman Geist <>
Betreff: Re: namd-l: problem in running targeted MD


Dear Norman,

thank you for your reply. The simulation is runnign well.

However, I have only one curiosity. How to deal if in a target structure some residues have not been crystallized?

I would simply leave 0.00 in the occupancy column, such that those heavy atoms will not be biased.

Is it correct?

Thank you






2016-02-25 23:57 GMT-08:00 Norman Geist < <> >:


Von: giulia palermo [ <> ]
Gesendet: Donnerstag, 25. Februar 2016 18:10
An: Norman Geist < <> >
Betreff: Re: namd-l: problem in running targeted MD


Hi Norman,


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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