[gmx-users] Water molecule can not be settled

[Ester Chiessi]

> > I verified that the 'incriminated' water is 4.11 angstrom far from the nearest atom of
> > the solute ( a quite hydrophilic polymer ), in the pdb of the last completed step.
> > This water is in the proximity of a face of the box.
>
> As David suggested, you might have this water spinning in a 'vacuum pocket'
> possibly due to a too low density of your system. Did you check that?
> I'm pretty sure all of the PBC bugs we had in the past, have been thorougly
> removed. There shouldn't be any new ones either... ;-) You *are* using
> a recent version, I assume?

The Gromacs version is 3.1.4.

When I used genbox at the beginning, the resulting density was 1071.1 g/l, in agreement
with the experimental value.

By an inspection with Insight, I can't see a possible 'vacuum pocket' in the last useful
frame.

Now, I used g_density to analize the density in the last structure before crash and I was
very surprised of the output:

 % g_density -f step982.pdb -s netmd14.tpr -o step982.xvg
...........
Reading file netmd14.tpr, VERSION 3.1.4 (double precision)
How many groups? 1
Opening library file /cineca/prod/gromacs-3.1.4/share/top/aminoacids.dat
Group     0 (      System) has  7564 elements
Group     1 (        ZZPV) has   384 elements
Group     2 (        ZZPL) has    32 elements
Group     3 (        ZZLH) has     8 elements
Group     4 (         SOL) has  7140 elements
Select a group: 0
Reading frame       0 time    1.000   There were 6 inconsistent shifts. Check your topology

 '', 7564 atoms
Last frame          0 time    1.000

Read 1 frames from trajectory. Calculating density

.............
% more step982.xvg
# This file was created by g_density
# which is part of G R O M A C S:
# GROtesk MACabre and Sinister
# All this happened at: Wed Mar 19 14:04:10 2003
#
@    title "Partial densities"
@    xaxis  label "Box (nm)"
@    yaxis  label "Density (kg/m\S3\N)"
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend "System"
           0              INF
      0.4272              INF
      0.8544              INF
      1.2816              INF
      1.7088              INF
       2.136              INF
      2.5632              INF
      2.9904              INF
      3.4176              INF
      3.8448              INF
%

What does it mean with 'INF'?
Thanks in advance.

Ester


--
Ester Chiessi
Dipartimento di Scienze e Tecnologie Chimiche
Universita' di Roma "Tor Vergata"
Via della Ricerca Scientifica
00133 Roma (Italy)
http://www.stc.uniroma2.it/cfmacro/cfmacroindex.htm
e-mail: ester.chiessi at uniroma2.it
Phone: 39*6*72594462
       39*6*72594874
Fax:39*6*72594328