[gmx-users] What exactly is the artifact caused by setting refcoord_scaling=no with position restraint

Christopher Neale chris.neale at mail.utoronto.ca
Wed Oct 31 17:55:48 CET 2012

I've asked the same question myself and would also like to know.

That said, there seems to be no issue if you set refcoord_scaling=com. According to the manual, this does
not give artefacts (whatever they are) and also does not change your restraint positions (as refcoord_scaling=all

Sorry that I can't give a complete answer, but, to my understanding, refcoord_scaling=no is probably just there
for backward compatibility and you should use refcoord_scaling=com.

Hopefully somebody who knows the full answer can comment.


-- original message -- 

After reading the manual and some earlier threads, I understand that this
would cause incorrect pressure and some "artifact". I found gromacs4.5.4
does not give warning while gromacs4.5.5 does?

But I wonder how large would the average pressure deviate when setting
refcoord_scaling=no compared when setting refcoord_scaling=com/ all, with
absolute position restraints? Does the pressure reported in .log file still
correct when setting refcoord_scaling=no?


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