It is all about order.
You have to include the position restraint .itp directly after the
molecule .itp (or inside the molecule.itp).
If you place it behind the solvent .itp it will assume the position
restraints refers to the solvent.
The atom numbers in the position restraint should match the
David,
> > I do not understand this.
> > Turning the restraints off is only affecting the highed of dG/dl
> and
> > turning it off means that you slowly go to zero.
>
> If you were computing a free energy of removing restraints,
> dG/dlambda
> should be negative, since it releases energy to tur
David,
> > Correct, but I made some changes to ensure correct storing of
> values in the
> > tpr file. Correct me if I am wrong, but the storage of these values
> only
> > occurs during the generation of a tpr file with grompp.
>
> Are you sure this worked properly? I tried to do this myself at o
I can tell if your only lambda dependence is in the>angle restraints, and you are using 3.3.1, you should be getting a>dv/dlambda that is zero everywhere, unless you've done something>strange like turning on soft core potentials or something.>DavidOn 5/11/06, Maarten Wolf <[EM
ree energy calculation? Are you
> changing the angle restraint as a function of lambda? If so, which
> way
> are you changing it? Decreasing or increasing restraints?
>
> David
>
>
>
> On 5/11/06, Maarten Wolf <[EMAIL PROTECTED]> wrote:
> > Dear users,
>
Dear users,
I have a small system with a number of small peptides. I want to
constraint the angle between the N-term to C-term vectors of different
peptides. This works well, but if I do a FEP calculation the dG/dl
becomes smaller than zero at some point.
I expected it to be at least allways grea
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