TMD Partial Fitting Problem

From: mert gölcük (
Date: Tue Jun 11 2019 - 07:26:02 CDT

Dear all,

What we want to do is to use a different set of atoms for fitted atoms and
biased atoms. As it is explained here

We set the altloc field for the fitted atoms to '1'.

The system has 186 residues. 125 alpha carbon atoms were fitted and 61 were
biased. When we run 50000 steps with 2 fs time step. The TMD spring
constant was 200 kcal/mol*A^2 and last step of the TMD was set 100000 (i.e.
the end of the simulation). Interestingly, The RMSD of the TMD atoms to the
target in the log file started with 0.115181 A and went to 0 in just 2000
steps. This issue happens in both NAMD-2.13-CUDA and NAMD-2.13-Multicore

Here we have to point out that the biased atoms are located in a rather
rigid part of the protein. In other words, if the biased 61 atoms are
aligned with their target directly then the RMSD is only 0.0005 A. What we
aim to observe is the TMD is the movement of this region of the protein
with respect to the remaining part.

>From what we see is that in our simulations the 125 atoms that are supposed
to be fitted are apparently not fitted. Or the TMD forces are not applied
in a sense so that it causes the region to move with respect to the
remaining of the protein. One solution to this might be to constrain the
fitted atoms, but I am more inclined to think that this shouldn’t be
required in the TMD simulations.

Any comments or suggestions would be greatly appreciated.

Initial RMSD values of the system were measured 1.54 Å for whole system,
6.06 Å for the whole protein, 19.21 Å for whole TMD domain and 33.54 Å for
biased atoms. After the simulation started, we were obtained 0.0113 and
0.115181 values from the log file and this values show that targetRMSD and
currentRMSD values respectively.

Thank you all.


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