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

[Hanne Antila]

Hi,

Yes, it does. Here is the output of  gmxcheck

 Item        #frames Timestep (ps)
Step         25001    0.004
Time         25001    0.004
Lambda       25001    0.004
Coords       25001    0.004
Velocities   25001    0.004
Forces       25001    0.004
Box          25001    0.004
Checking coordinate file nvt_sample.tpr
Reading file nvt_sample.tpr, VERSION 4.5.5 (double precision)
Reading file nvt_sample.tpr, VERSION 4.5.5 (double precision)
2048 atoms in file
coordinates found
box         found
velocities  found

Kinetic energy: 3649.82 (kJ/mol)
Assuming the number of degrees of freedom to be Natoms * 3 or Natoms * 2,
the velocities correspond to a temperature of the system
of 142.894 K or 214.341 K respectively.

and a sample of the .gro for reference:

Generated by trjconv : H20 tip4p t=   0.00000
 2048
    1SOL     OW    1   0.899   0.254   1.534 -0.4616  0.2534  0.2217
    1SOL    HW1    2   0.951   0.310   1.476  1.7867 -0.6432  1.3081
    1SOL    HW2    3   0.917   0.288   1.622 -1.0807 -0.5764  0.6743
    1SOL     MW    4   0.907   0.263   1.537 -0.2878  0.0692  0.3859
    2SOL     OW    5   0.270   2.394   0.072 -0.4689 -0.1951 -0.0554
    2SOL    HW1    6   0.202   2.346   0.120  0.5258 -1.4470  0.1173
    2SOL    HW2    7   0.326   2.431   0.140  0.1427 -0.8067 -0.2207
    2SOL     MW    8   0.269   2.393   0.084 -0.2976 -0.3939 -0.0546

Yours,

Hanne


2014/1/19 Mark Abraham <mark.j.abraham at gmail.com>

> Hi,
>
> That does sound strange. Does gmxcheck show that the original .trr has
> velocities?
>
> Mark
> On Jan 19, 2014 2:16 AM, "Antila Hanne" <hanne.antila at aalto.fi> wrote:
>
> > Dear experts,
> >
> > I converted a trajectory (.trr) containing a simulation of tip4ew water
> >  to .gro format. In the resulting .gro file, there are velocities also
> for
> > the tip4 virtual sites MW. This confuses me, since these sites have no
> > mass. How is this velocity calculated? I have been under the impression
> > that, at each step, the coordinates of MW are merely assigned based on
> the
> > coordinates of the rest of the water atoms.
> >
> > Help will be appreciated!
> >
> > Yours,
> >
> > Hanne Antila
> >
> > PhD candidate,
> > Aalto University
> > --
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