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

[sumanc]

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:

oplsaa.f:
 opls_115   MW  0      0.00000    -1.040       D    0.00000e+00  0.00000e+00

gromos43a2.ff:
   IW      0  0.000      0.000     D           0           0

charmm27.ff:
MWT4    0       0.000000        -1.04   A       0.0     0.0     ; TIP4p
vsite

amber03.ff
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,
Suman.


On Sun, Jan 19, 2014 at 9:59 PM, Antila Hanne [via GROMACS] <
ml-node+s5086n5013883h7 at n6.nabble.com> wrote:

> 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 <[hidden email]<http://user/SendEmail.jtp?type=node&node=5013883&i=0>>
>
>
> > Hi,
> >
> > That does sound strange. Does gmxcheck show that the original .trr has
> > velocities?
> >
> > Mark
> > On Jan 19, 2014 2:16 AM, "Antila Hanne" <[hidden email]<http://user/SendEmail.jtp?type=node&node=5013883&i=1>>
> 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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