Repository 'gmx_trj'
hg clone https://toolshed.g2.bx.psu.edu/repos/chemteam/gmx_trj

Changeset 11:240834a8b602 (2021-12-21)
Previous changeset 10:95fa9dfbc4bb (2021-12-01) Next changeset 12:aefa274e0126 (2022-03-14)
Commit message:
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit a8eac146d0f6b9696f4afaaaa96891e8e324f78e"
added:
test-data/oplsaa.ff-tip4p.itp
b
diff -r 95fa9dfbc4bb -r 240834a8b602 test-data/oplsaa.ff-tip4p.itp
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/oplsaa.ff-tip4p.itp Tue Dec 21 13:43:35 2021 +0000
[
@@ -0,0 +1,52 @@
+;
+; Note the strange order of atoms to make it faster in gromacs.
+;
+[ moleculetype ]
+; molname nrexcl
+SOL 2
+
+[ atoms ]
+; id at type res nr  residu name at name cg nr charge
+1       opls_113        1       SOL      OW     1       0.0
+2       opls_114        1       SOL     HW1     1       0.52
+3       opls_114        1       SOL     HW2     1       0.52
+4       opls_115        1       SOL      MW     1      -1.04
+
+#ifndef FLEXIBLE
+[ settles ]
+; OW    funct   doh        dhh
+1       1       0.09572    0.15139
+#else
+[ bonds ]
+; i j funct length force.c.
+1 2 1 0.09572 502416.0 0.09572 502416.0 
+1 3 1 0.09572 502416.0 0.09572 502416.0 
+
+[ angles ]
+; i j k funct angle force.c.
+2 1 3 1 104.52 628.02 104.52 628.02
+#endif
+
+[ exclusions ]
+1 2 3 4
+2 1 3 4
+3 1 2 4
+4 1 2 3
+
+; The position of the virtual site is computed as follows:
+;
+; O
+;         
+;      D
+;   
+; H H
+;
+; const = distance (OD) / [ cos (angle(DOH))  * distance (OH) ]
+;   0.015 nm / [ cos (52.26 deg) * 0.09572 nm ]
+
+; Vsite pos x4 = x1 + a*(x2-x1) + b*(x3-x1)
+
+[ virtual_sites3 ]
+; Vsite from funct a b
+4 1 2 3 1 0.128012065 0.128012065
+