[gmx-users] Position restrains during alchemical transformation

Mark Abraham mark.j.abraham at gmail.com
Wed Aug 9 11:48:57 CEST 2017


I presume the position-restraints file was written by a tool that didn't
anticipate this use case (and pdb2gmx likely does not). If so, I would edit
my position restraints file to express my intent, ie copy the functype and
parameters so that there's an A and B state on the same line, just as with
other topology pieces.

One could also use grompp -maxwarn, but laziness leads to hate, and hate
leads to the Dark Side. You will one day curse Past Hermann, because a
warning you ignored costs you months of wasted simulation time.


On Wed, Aug 9, 2017 at 11:27 AM Hermann, Johannes <
J.Hermann at lrz.tu-muenchen.de> wrote:

> Dear all,
> I have a questions concerning MD free energy calculations using
> alchemical tranformation. I want to restrain the backbone of my protein
> which I mutate during TI. However, I do not know how to correctly
> generate position restrains. If I use the position restrain file, which
> I generated for the A state, following warning shows up:
> WARNING 1 [file posre.itp, line 1470]:
>    Some parameters for bonded interaction involving perturbed atoms are
>    specified explicitly in state A, but not B - copying A to B
> Can I ignore this warning, or do you have any suggestions for me?
> All the best and thank you very much in advance
> Johannes
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