Dear Teodoro,<br>I'm running QM/MM cp2k on a pretty big system.<br>I'm using amber topology so I need a way to SHAKE the water molecules<br>I
understand I do it in the &MOTION section with something like that,
using molecule as, without a psf I cannot specify the molname <br><br> &CONSTRAINT<br> &G3X3<br> MOLECULE 31<br> DISTANCES 1.7958 1.7958 2.85444<br> ATOMS 1 2 3<br> EXCLUDE_QM<br> &END G3X3<br> &END CONSTRAINT<br><br>Here
31 is the molecule kind number of the fist water molecule as guessed
from the output of a tentative run with verbose output: I get the
molecule kind name is MOL30 and the molecule kind number is 31: is it
right?<br><br> 31. Molecule kind: MOL30 Number of atoms: 3<br> Atom Atomic kind name<br> 1 OW<br> 2 HW<br> 3 HW<br><br> The name was automatically generated: T<br> Number of molecules: 1<br> Molecule list: 31<br> Number of bonds: 3<br><br><br><br>The
problem is that I have 47883 water molecules: do I have to repeat this
CONSTRAINT section (or the &G3X3 subsection ) 50 thousand time? the
input would be pretty big.<br>Is there a clever way to SHAKE water molecules in my case?<br><br>you write in your previous answer <br>MOLECULE 1..15<br><br>but
from the manual I understand MOLECULE takes only one integer: what does
your line mean? can I specify for a range instead then for a single
molecule?<br><br>Is it possible to have the code recognizing a MOLNAME also when one uses an amber topology?<br>I
am forced to use amber topology as I did not find the ambertocharmm
converter (leap2fist ?) anymore and I have to shake water, of course.<br><br>More in general: what do you mean by "molecule"?<br>each residue of a protein is assigned to a "molecule": what is the meaning of that?<br>TOPOLOGY > <a href="http://cp2k.berlios.de/manual/CP2K_INPUT/FORCE_EVAL/SUBSYS/TOPOLOGY.html#list_PARA_RES" id="desc_PARA_RES">PARA_RES</a> is set to TRUE<br>what if I set it to FALSE?<br>I
get the term molecule has nothing to do with its chemical meaning, but
my protein part is composed by more than one sub-units: does that
conflicts with <a href="http://cp2k.berlios.de/manual/CP2K_INPUT/FORCE_EVAL/SUBSYS/TOPOLOGY.html#list_PARA_RES" id="desc_PARA_RES">PARA_RES</a> FALSE?<br>Then I get some strange molecules as well like <br> 1. Molecule kind: _QM_MOL0 Number of atoms: 10657<br>this is not the QM part, nor the QM + link and I am lost <br><br>thanks for the help<br>m<br><br><br>