[gmx-users] TIP4ew water and velocities on dummy atoms

sumanc chakrabarty.suman at gmail.com
Thu Jan 30 10:09:55 CET 2014

Dear all,

I have a similar observation regarding the dummy atom in TIP4P-based water
models (the velocities being calculated/written to trr files). In addition,
I notice that some force fields mark the dummy atom in TIP4P as atom type
"D", and some mark them as "A". But the behavior of calculating/writing
velocities for dummy atoms seem to be same across all of them.

Here are the corresponding lines from the ffnonbonded.itp file for various
force fields:

 opls_115   MW  0      0.00000    -1.040       D    0.00000e+00  0.00000e+00

   IW      0  0.000      0.000     D           0           0

MWT4    0       0.000000        -1.04   A       0.0     0.0     ; TIP4p

MW           0       0.0000  0.0000  A   0.00000e+00  0.00000e+00

So it seems the dummy atom is marked as "atom" (type A) in both charmm27 and
amber03 force fields. Is this correct? Will the position of the dummy atom
still be calculated correctly? Please confirm. Thanks.

Best regards,

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