Re: [gmx-users] v-rescale fatal error

Kester Wong Fri, 10 Oct 2014 23:06:03 -0700

Hi Mark,

The H3O ion topology is defined as follows:

; Hydronium and hydroxide parameters developend by M.G. Wolf

; Hydronium

[ moleculetype ]

; molname nrexcl

H3O 2

[ atoms ]

; id at type res nr residu name at name cg nr charge mass

1 SWM4-NDP_O2 1 H3O O2 1 0.852

2 SWM4-NDP_110b 1 H3O OA 1 -1.124 ; modified

3 SWM4-NDP_H2 1 H3O H31 1 0.424

4 SWM4-NDP_H2 1 H3O H32 1 0.424

5 SWM4-NDP_H2 1 H3O H33 1 0.424

[ polarization ]

#ifdef POL2WATER

1 2 2 0.0004195 0.02 16.736e8

#else

1 2 1 0.0004195

#endif

; Initialy developed as a harmonic bond

; Conversion: alpha=sqrt(qS)/(4*pi*eps0*CAL2J*A2NM*k) = 138.9354492 * sqrt(qS)/k

; [ bonds ]

; 1 2 6 0 418400

#ifdef FLEXIBLE

[ bonds ]

1 3 1 0.102 400000

1 4 1 0.102 400000

1 5 1 0.102 400000

[ angles ]

3 1 4 1 109.47 400

3 1 5 1 109.47 400

4 1 5 1 109.47 400

#else

[ constraints ]

; i funct doh dhh

1 3 1 0.102

1 4 1 0.102

1 5 1 0.102

3 4 1 0.169124

4 5 1 0.169124

3 5 1 0.169124

#endif

[ exclusions ]

1 2 3 4 5

2 1 3 4 5

3 1 2 4 5

4 1 2 3 5

5 1 2 3 4

For example, within the SWM4-NDP system containing 2 ions that I have defined, I get something like this:

Number of degrees of freedom in T-Coupling group GRA is 0.00

Number of degrees of freedom in T-Coupling group SOL is 11985.00

Number of degrees of freedom in T-Coupling group H3O is 9.00

Number of degrees of freedom in T-Coupling group Cl- is 3.00

I was able to then obtain the .tpr file, however, once the job is submitted, the fatal error reads:

Inner product between old and new vector <= 0.0!

constraint #5 atoms 46282 and 46283

Wrote pdb files with previous and current coordinates

Inner product between old and new vector <= 0.0!

constraint #4 atoms 46281 and 46283

Back Off! I just backed up step0b.pdb to ./#step0b.pdb.1#

Back Off! I just backed up step0c.pdb to ./#step0c.pdb.1#

Wrote pdb files with previous and current coordinates

starting mdrun 'Water with ions'

5000000 steps, 5000.0 ps.

Inner product between old and new vector <= 0.0!

constraint #5 atoms 46282 and 46283

Back Off! I just backed up step0b.pdb to ./#step0b.pdb.2#

Back Off! I just backed up step0c.pdb to ./#step0c.pdb.2#

Wrote pdb files with previous and current coordinates

-------------------------------------------------------

Program gmx_mpi, VERSION 5.0

Source code file: /share/gromacs-5.0/src/gromacs/mdlib/coupling.c, line: 1439

Fatal error:

The v-rescale thermostat was called with a group with #DOF=2.999250, but for #DOF<3 only integer #DOF are supported

For more information and tips for troubleshooting, please check the GROMACS

website at http://www.gromacs.org/Documentation/Errors

-------------------------------------------------------

The SWM4-NDP file can be downloaded directly from virtualchemistry.org

Cheers,

Kester

--------- 원본 메일 ---------

보낸사람 : Mark Abraham <mark.j.abra...@gmail.com>
받는사람 : Discussion list for GROMACS us <gmx-us...@gromacs.org>
받은날짜 : 2014년 10월 10일(금) 21:35:03
제목 : Re: [gmx-users] v-rescale fatal error

Hi Kester,

Glad it's resolved. I am curious what (H3O+?) molecule definition led to
that computation of the DOF? That code is not tested at all...

Mark

On Fri, Oct 10, 2014 at 2:03 PM, Kester Wong  wrote:

> Hi Justin and all,
>
>
> The same mistake will not be repeated.
>
> The ions are now defined in the residuetypes.dat file and should be
> grouped together.
>
>
>
> -From lessons learned, comes better performance.
>
> Thank you all.
>
> Kester
> --------- 원본 메일 ---------
>
> *보낸사람* : Justin Lemkul 
> *받는사람* : 
> *받은날짜* : 2014년 10월 10일(금) 20:38:56
> *제목* : Re: [gmx-users] v-rescale fatal error
>
> On 10/10/14 7:36 AM, Kester Wong wrote:
> > Hi Mark,
> >
> >
> > I think it was due to the charged groups in  my temp. coupling setting; I had
> > the H3O cation(s) and Cl anion(s) grouped separately:
> >
> > tc-grps                  = GRA SOL H3O Cl-
> >
> > ; Time constant (ps) and reference temperature (K)
> >
> > tau-t                    = 0.5 0.5 0.5 0.5
> >
> > ref-t                    = 300 300 300 300
> >
> >
> > Calculations run fine once I grouped the ions together, or water+ions.
> >
>
> You shouldn't couple ions separately from the solvent; that's just not stable.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
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Re: [gmx-users] v-rescale fatal error

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