[gmx-users] Energy minimization problem with Double precision and mpi

[Josiah Zayner]

-----Original Message-----
From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
On Behalf Of David van der Spoel
Sent: Saturday, June 23, 2007 4:36 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Energy minimization problem with Double precision
andmpi

Josiah Zayner wrote:
> I managed to install mdrun_d from CVS and the problem is fixed....


>>you didn't say which cvs solved your problem. was it the 
>>release_3_3_patches branch?

Mdrun_d says version: 3.3.99_development_20070413
It was the main branch.

> 
> -----Original Message-----
> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
> On Behalf Of Josiah Zayner
> Sent: Saturday, June 23, 2007 1:05 PM
> To: gmx-users at gromacs.org
> Subject: [gmx-users] Energy minimization problem with Double precision and
> mpi
> 
> Each time I try to run mdrun with double precision and more than one node,
I
> always receive some atom with infinite Fmax, no matter what I do, Always
on
> Step=0. The strangest thing is that it still attempts the minimization but
> the values never change except for Dmax in a steepest descent. If I change
> the coordinates of the atom that has the inf value another one has
infinite
> value and so on. I use lam/mpi, with the command 'mpirun -np 5 mdrun_d -v
> -deffnm potd'. My double precision was configured with both --enable-mpi
and
> --enable-double. Here is a copy of the mdp file I use:
> 
> title			=   potd
> cpp			=   /usr/bin/cpp
> constraints		=   none
> integrator		=   steep
> nsteps			=   0  
> ns_type			=   grid
> nstcomm			=   1
> nstlist			=   10
> rlist			      =   1.4
> coulombtype		      =   Shift
> vdw_type			=   Shift
> rcoulomb			=   1.2
> rvdw				=   1.2
> rcoulomb_switch		=   1.0
> rvdw_switch			=   1.0
> epsilon_r			=   6.0	
> optimize_fft		=   yes
> 	
> 
> emtol			=   1000
> emstep		=   0.01
> nstcgsteep		=   100
> 
> It doesn't matter if it is in vaccum or water. I have minimized to an
emtol
> of 10 and mdrun_d still does not work. I am using gromacs 3.3.1. I have
> tried changing or removing almost every value in the mdp file. I have
tried
> different pdb files. Tried using grompp and grompp_d. Tried with -sort
> -shuffle and without. Is this another one of those compiler issues like
> genion? Any help would be great.
> 
> Thanks,
>     Josiah Zayner 
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
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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