Subject: Re: Re: [gmx-users] Gromacs 4 bug?

[Bernhard Knapp]

Mark wrote:

> What's happening in the log files? What's the latest information in the 
> checkpoint files? Could there be some issue with file system availability?

Hi Mark

Unfortunaltey I already deleted the simulation files which got stuck 
after 847ps. But here is the output of another simulation done on the 
same system but with an other pdb file. This one gets stuck after 179ps 
with the following output:

The latest thing the checkpoint file says is:

"imb F  3% step 89700, will finish Wed Jul  1 09:11:00 2009
imb F  3% step 89800, will finish Wed Jul  1 09:02:51 2009"

The predcition for 1st of July is not surprising since I am always 
parameterizing the simulation with 200ns to avoid to restart it if 
something interesting happens in the last frames.

for the .log file it is:

"Writing checkpoint, step 88000 at Thu Dec 11 16:34:31 2008

   Energies (kJ/mol)
       G96Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
    7.83753e+03    3.64068e+03    2.45951e+03    1.29167e+03    5.13688e+04
        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential    Kinetic En.
    3.82346e+05   -2.48883e+06   -3.51313e+05   -2.39119e+06    4.57648e+05
   Total Energy    Temperature Pressure (bar)  Cons. rmsd ()
   -1.93355e+06    3.10014e+02    1.09267e-01    2.14030e-05

DD  step 88999 load imb.: force  3.1%

           Step           Time         Lambda
          89000      178.00002        0.00000

   Energies (kJ/mol)
       G96Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
    8.03089e+03    3.59681e+03    2.42628e+03    1.20942e+03    5.12341e+04
        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential    Kinetic En.
    3.81539e+05   -2.48602e+06   -3.51307e+05   -2.38929e+06    4.56901e+05
   Total Energy    Temperature Pressure (bar)  Cons. rmsd ()
   -1.93239e+06    3.09508e+02    1.64627e+01    2.08518e-05"


the disk is also free df -h says  2.3G out of 666G used.

The only difference between the system with gromacs 3.3 and gromacs 4 is 
that gromacs 4 is running under suse 11 while gromacs 3.3 is running on 
a node with suse 10. But I dont think this can be the problem?

cheers
Bernhard