[gmx-developers] grompp and vsites

[David van der Spoel]

Michel Cuendet wrote:
> Hi all,
> 
> The last CVS version of grompp seems not to be working properly on 32bit 
> machines in conjunction with vsites. I haven't tried to download the 
> current GIT version yet, please tell me if there have been any updates. 
> In the following, I use the gmx CVS version downloaded on 12.6.2009. 
> Compilers and architecture are indicated below.
> 
> On a 32bit machine :
>    $there/i686_gcc4.2.4/grompp -p $base_run/topol.top -c 
> $base_run/equil/confout.gro -t $base_run/equil/traj.trr  -f 
> $base_run/prod/grompp.mdp -o topol32.tpr >& grompp32.log
> 
> On a 64 bit machine :
>    $there/em64t_gcc3.4.6/bin/grompp -p $base_run/topol.top -c 
> $base_run/equil/confout.gro -t $base_run/equil/traj.trr  -f 
> $base_run/prod/grompp.mdp -o topol64.tpr >& grompp64.log
> 
> grompp64.log is similar to what the 4.0.4 version gives. But 
> grompp32.log shows incorrect behavior. It lacks the "Cleaning up 
> constraints and constant bonded interactions with virtual sites" section 
> for chains B and C (there are 3 chains in my system, A, B, C).
> 
> Also the tpr file produced on a 32 bit machine is not correct. Comparing 
> topol64.tpr with the tpr file created with earlier versions of grompp 
> indicates no differences. However,
> 
>    gmxcheck -s1 topol32.tpr -s2 topol64.tpr
> [... usual output ...]
> comparing inputrec
> inputrec->rgbradii (1.000000e+00 - 2.000000e+00)
> inputrec->gb_dielectric_offset (9.000000e-03 - 9.000000e-02)
> inputrec->sa_algorithm (0 - 1)
> inputrec->nstdhdl (10 - 1)
> comparing top
> comparing idef
> idef->ntypes (1343 - 1316)
> idef->functype[850][850] (13 - 4)
> idef->iparam[850]1: theta= 1.09500000e+02, ktheta= 3.68191986e+02, r13= 
> 0.00000000e+00, kUB= 0.00000000e+00
> idef->iparam[850]2: theta= 0.00000000e+00, ktheta= 0.00000000e+00, r13= 
> 0.00000000e+00, kUB= 0.00000000e+00
> idef->iparam[851]1: theta= 1.09500000e+02, ktheta= 2.51039993e+02, r13= 
> 2.07399994e-01, kUB= 1.67360000e+04
> idef->iparam[851]2: theta= 1.07500000e+02, ktheta= 4.30951996e+02, r13= 
> 0.00000000e+00, kUB= 0.00000000e+00
> [... lots of output ...]
> 
> 
> Furthermore, if you try to read an energy file with the 32bit version of 
> grompp, you get a Segmentation Fault, whereas the 64bit version of 
> grompp is fine.
> 
>    grompp -p $base_run/topol.top -c $base_run/equil/confout.gro -t 
> $base_run/equil/traj.trr -e $base_run/equil/ener.edr -f 
> $base_run/prod/grompp.mdp -o topol32bis.tpr
> [ ... usual output ... ]
> Reading Coordinates, Velocities and Box size from old trajectory
> Will read whole trajectory
> trn version: GMX_trn_file (single precision)
> Last frame          4 time 1200.000
> Using frame at t = 1200 ps
> Starting time for run is 0 ps
> Note: enx file_version 1, software version 2
> Opened ../../dyna/AA_1//equil/ener.edr as single precision energy file
> Note: enx file_version 1, software version 2
> Segmentation fault

This doesn't look good. Are you certain compilation went fine? Did you 
run the test set?
Did you compile double and single from exactly the same source? And did 
you run make distclean in between?
The only other thing I can think of is that there were strange 
characters in the mdp file.
> 
> Cheers,
> Michel
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Professor of Biology
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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