[gmx-users] Position restrains during alchemical transformation

Hermann, Johannes J.Hermann at lrz.tu-muenchen.de
Thu Aug 10 14:33:59 CEST 2017

Hi Mark,

thank you for your answer. It works. I used genrestr for generating the 
position restrains. I now manually edited the respective lines. Gromacs 
wants only the parameters for the B state (If you repeat the function 
type you get an error).


123    1    1000   1000   1000   1000   1000   1000

All the best and thanks again


On 09.08.2017 11:48, Mark Abraham wrote:
> Hi,
> 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.
> Mark
> 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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*Technische Universität München*
*Johannes Hermann, M.Sc.*
Lehrstuhl für Bioverfahrenstechnik
Boltzmannstr. 15
D-85748 Garching
Tel: +49 8928915730
Fax: +49 8928915714

Email: j.hermann at lrz.tum.de

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