[gmx-users] Re: Re: unusually long run required

[jaimin at iitb.ac.in]

Dear Users,
I am stuck.
There is no md.log file generated in folder in which I carry out mdrun.
There are only em.log and pr.log files (I use the format of the example
given for Ribonuclease S peptide on the "getting started" page.)

A part of the em.log file has:
------------------------------------------------------------------------------
STEEPEST DESCENTS
   Tolerance = 2000
Grid: 16 x 18 x 18 cells

Testing x86 processor CPUID...

Testing x86 SSE capabilities...

Testing x86 3DNow capabilities...
CPU and OS support SSE.
Using Gromacs SSE assembly innerloops.
---------------------------------------------------------------------------


This suggests to me that the simulation does use SSE.
Similarly, in the pr.log file:
---------------------------------------------------------------------------Started
mdrun on node 0 Thu Feb 3 16:36:25 2005
Initial temperature: 299.701 K
Grid: 16 x 18 x 18 cells

Testing x86 processor CPUID...

Testing x86 SSE capabilities...

Testing x86 3DNow capabilities...
CPU and OS support SSE.
Using Gromacs SSE assembly innerloops.
--------------------------------------------------------------------------

So why should it then take so long?

I am ready to wait for a few days if that is required. However, when I
change the default settings to:
nsteps = 1250000 ; total 2500 ps.
nstxout = 250000

I do not get the trajectory moving and I see the following in the
terminal:
---------------------------------------------------------------------------
Reading file pr.tpr, VERSION 3.0.5 (single precision)
trn version: GMX_trn_file
Last frame -1 time 0.000
WARNING: Incomplete frame: nr 0 time 0
Opening library file /usr/local/share/gromacs/top/aminoacids.dat
Opening library file /usr/local/share/gromacs/top/export.dlg
Opening library file /usr/local/share/gromacs/top/bonds.dlg
Opening library file /tmp/fileRrDpgj
Reading file pr.tpr, VERSION 3.0.5 (single precision)
Reading file pr.tpr, VERSION 3.0.5 (single precision)
Last frame -1 time 0.000
WARNING: Incomplete frame: nr 0 time 0
Opening library file /usr/local/share/gromacs/top/vdwradii.dat
Last frame -1 time 0.000
WARNING: Incomplete frame: nr 0 time 0
Last frame -1 time 0.000
----------------------------------------------------------------------------

I do get the trajectory with the default settings. Why should that be?