Robert
I think, I cant help you too much, cause your problem involves too many
sources of errors.
Your topology (if continued that way) seems to be ok.
Your TI-params seem to be ok, too.
First, make clear: Do you use Position RESTRAINTS or (distance)
CONSTRAINTS. There is a fundamental difference.
Second you should be aware of how to get out the restraint/constraint
term from your free energy, to get a correct one. Don't ask me how, I
don't know ;)
Second, I suppose, your restraints/constraints are wrong somehow. Please
give some info about the restraints/constraints and the mdp-entries, you
use.
I'm really wondering about the distortion of your base, cause this must
not happen if you perturb the bonded terms the way, you describe.
Be aware, that, if you position restraint with e.g. posre.itp,
B-parameters should be available there, too. I don't really know, if the
A-parameters in the posre-file will be copied to B, too. Test that with
a gmxdump.
Regards
Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Germany
Tel. : ++49 551 201 2310
Fax : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
mgoette2[at]gwdg.de
WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/
Robert Johnson wrote:
Hello everyone,
I'm computing the free energy of binding of a DNA base on a carbon
nanotube. I think it's a pretty simple calculation and I'm proceeding
in a very standard way. This is what I'm doing:
I have the optimal orientation of the base on the nanotube. I'm
constraining the positions of the base atoms with a soft harmonic
potential.
I then am running two different FEP calculations: one where I turn off
the charges on the base atoms and a second where I then turn off all
the lennard-jones parameters for the base atoms. For each of these I
use the following:
delta_lambda = 0
sc_alpha = 0.7
sc_power = 1
sc_sigma = 0.3
I run a series of trajectories at constant lambda values from 0 to 1.
However, I notice some problems with the trajectories when I turn off
the LJ parameters. As lambda is varied from 0 to 1, it seems that the
position restraints no longer are being applied. Additionally, the DNA
base geometry starts to become severely distorted at lambda values
greater than about 0.6. This happens despite the fact that I am not
perturbing the internal bonded interactions of the base. Here is a
sample of my topology (included just the first line of each section):
[ moleculetype ]
; Name nrexcl
dg-disappear 3
[ atoms ]
1 P 1 DG P 1 1.1659 30.9700
DUM 0.0000 30.9700
...
[ bonds ]
1 2 1 0.1480 439320.0000 0.1480 439320.0000
...
[ angles ]
1 4 5 1 120.5001 836.8000
120.5001 836.8000
...
[ dihedrals ]
1 4 5 8 1 0.0000 1.6039 3
0.0000 1.6039 3
...
[ position_restraints ]
1 1 100 100 100 100 100 100
...
So you can see that I am not perturbing the bonded interactions as I
have just copied the same values from topology A.
Also, I am experiencing additional problems when lambda=1. After about
2ns, all the motion in the system begins to freeze and all the atoms
simply vibrate about a fixed position. Soon after that the simulation
crashes.
Can anyone comment on what's going on here?
Thanks,
Bob Johnson
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