Mark Abraham wrote:
Justin M. Shorb wrote:
Greetings!
I have been running gromacs to simulate a chromophore (NMAd) in water.
I have verified that the coulombic force is calculated correctly by
doing a rerun of the simulation trajectory and extracting the forces
from a forcefield of vanishing force constants (thus removing all vdW
and bonded terms). This works, although it is fairly brute-force.
Now, I am trying to scale up and look at a single peptide Amide-I band
in a transmembrane protein. Unfortunately, if I use the same mdp file,
I get different results than if I use the mdp file with which the
production run was generated.
I don't understand your meaning here.
By gmxdump-ing the tpr files, I can figure out the differences between
the run files. I verified that varying PME parameters cause a
negligible effect, and most of the basic I/O parameters of course
shouldn't matter.
The biggest difference between the two files is that one reports zero
for the multinr and uses nr=0 and nra=0, whereas the other tpr file
reports 123 for the multinr, nr=123, nra=6326, and then specifies
blocks[SBLOCKS][...]
Um, no there are huge differences here. One uses temperature and
pressure coupling and the other doesn't. One has cut-offs at 1.4nm, the
other 1nm. There's many more as well....
Mark
I agree with mark here. Very different topologies, not just the force
constants. In addition you do not specify clearly what is the difference
in result that you observe, i.e. between what and what. PME does not use
energy groups.
--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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