On 12/01/2012 9:14 PM, Matthias Ernst wrote:
Hi,
I have some questions.
First, what dihedral angles will Gromacs produce and use in topology
when simulating proteins? To be more specific, I was looking for psi
(N-C(a)-C-N) and phi (C-N-C(a)-C) angles in all the dihedrals that
were generated by pdb2gmx. I only found the psi angles but not phi. Is
that by purpose?
If your force field doesn't implement such dihedrals, then they won't be
there. However it seems to me more likely that you aren't looking in
enough right places. Consider the opposite order of the atom numbers, also.
Second, for testing purposes, I want to do single point energy
calculations in vacuo with no cutoffs at given coordinates. When I use
an mdp like the one below, it always changes the coordinates slightly
but enough to change the energy values noticeably. Is there a better
way to to this?
Zero-step MD is a way to do this. Using constraints = none, or
continuation = yes will stop slight changes from the use of constraints.
Another alternative is using mdrun -rerun, which is efficient for doing
many such evaluations, and guarantees no changes to the coordinates.
Third, I'm not sure if the coordinates are used correctly. To compare
the energy values, I inserted a little piece of code in the energy
evaluation routines which outputs the coordinates of all atoms. It
seems that everything beyond the three digits after the decimal sign
in the .gro files is filled with arbitrary numbers. I know that using
floating point data types results in a loss of accuracy but I thought
even with single precision, the accuracy should be higher than three
digits?
The accuracy is as high as it can be - I think you're assuming nothing
has happened, and that isn't quite true.
Mark
Here is my mdp:
constraints = all-bonds
integrator = MD
nsteps = 0
nstcomm = 1
ns_type = grid
rlist = 0.0
rcoulomb = 0.0
rvdw = 0.0
Tcoupl = no
Pcoupl = no
gen_vel = no
pbc = no
I would greatly appreciate any help and comments.
Best regards,
Matthias Ernst
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