<p style="border:0; padding:0; margin:0; font-family:'Gulim'; font-size:10pt; cursor: text;"><p style="font-family: Gulim; font-size: 10pt; border: 0px; padding: 0px; margin: 0px; cursor: text;">Hi Mark, </p><p style="font-family: Gulim; font-size: 10pt; border: 0px; padding: 0px; margin: 0px; cursor: text;"><br></p><p style="font-family: Gulim; font-size: 10pt; border: 0px; padding: 0px; margin: 0px; cursor: text;">The H3O ion topology is defined as follows:</p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;">; Hydronium and hydroxide parameters developend by M.G. Wolf</p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;">; Hydronium</p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;">[ moleculetype ]</p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;">; molname nrexcl</p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;">H3O 2</p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;"><br></p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;">[ atoms ]</p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;">; id at type res nr residu name at name cg nr charge mass</p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;">1 SWM4-NDP_O2 1 H3O O2 1 0.852</p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;">2 SWM4-NDP_110b 1 H3O OA 1 -1.124 ; modified</p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;">3 SWM4-NDP_H2 1 H3O H31 1 0.424</p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;">4 SWM4-NDP_H2 1 H3O H32 1 0.424</p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;">5 SWM4-NDP_H2 1 H3O H33 1 0.424</p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;"><br></p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;">[ polarization ]</p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;">#ifdef POL2WATER</p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;">1 2 2 0.0004195 0.02 16.736e8</p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;">#else</p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;">1 2 1 0.0004195</p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;">#endif</p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;"><br></p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;">; Initialy developed as a harmonic bond</p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;">; Conversion: alpha=sqrt(qS)/(4*pi*eps0*CAL2J*A2NM*k) = 138.9354492 * sqrt(qS)/k</p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;">; [ bonds ]</p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;">; 1 2 6 0 418400</p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;"><br></p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;">#ifdef FLEXIBLE</p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;">[ bonds ]</p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;">1 3 1 0.102 400000</p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;">1 4 1 0.102 400000</p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;">1 5 1 0.102 400000</p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;"><br></p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;">[ angles ]</p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;">3 1 4 1 109.47 400</p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;">3 1 5 1 109.47 400</p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;">4 1 5 1 109.47 400</p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;"><br></p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;">#else</p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;">[ constraints ]</p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;">; i funct doh dhh</p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;">1 3 1 0.102</p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;">1 4 1 0.102</p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;">1 5 1 0.102</p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;">3 4 1 0.169124</p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;">4 5 1 0.169124</p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;">3 5 1 0.169124</p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;">#endif</p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;"><br></p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;">[ exclusions ]</p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;">1 2 3 4 5</p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;">2 1 3 4 5</p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;">3 1 2 4 5</p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;">4 1 2 3 5</p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;">5 1 2 3 4</p><div><br></div><p style="font-family: Gulim; font-size: 10pt; border: 0px; padding: 0px; margin: 0px; cursor: text;"><br></p><p style="font-family: Gulim; font-size: 10pt; border: 0px; padding: 0px; margin: 0px; cursor: text;"><br></p><p style="font-family: Gulim; font-size: 10pt; border: 0px; padding: 0px; margin: 0px; cursor: text;">For example, within the SWM4-NDP system containing 2 ions that I have defined, I get something like this:</p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;">Number of degrees of freedom in T-Coupling group GRA is 0.00</p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;">Number of degrees of freedom in T-Coupling group SOL is 11985.00</p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;">Number of degrees of freedom in T-Coupling group H3O is 9.00</p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;">Number of degrees of freedom in T-Coupling group Cl- is 3.00</p><div style="font-family: Gulim; font-size: 10pt;"><br></div><div style="font-family: Gulim; font-size: 10pt;">I was able to then obtain the .tpr file, however, once the job is submitted, the fatal error reads:</div><div style="font-family: Gulim; font-size: 10pt;"><br></div><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;">Inner product between old and new vector <= 0.0!</p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;">constraint #5 atoms 46282 and 46283</p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;">Wrote pdb files with previous and current coordinates</p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;">Inner product between old and new vector <= 0.0!</p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;">constraint #4 atoms 46281 and 46283</p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;"><br></p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;">Back Off! I just backed up step0b.pdb to ./#step0b.pdb.1#</p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;"><br></p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;">Back Off! I just backed up step0c.pdb to ./#step0c.pdb.1#</p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;">Wrote pdb files with previous and current coordinates</p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;">starting mdrun 'Water with ions'</p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;">5000000 steps, 5000.0 ps.</p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;">Inner product between old and new vector <= 0.0!</p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;">constraint #5 atoms 46282 and 46283</p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;"><br></p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;">Back Off! I just backed up step0b.pdb to ./#step0b.pdb.2#</p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;"><br></p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;">Back Off! I just backed up step0c.pdb to ./#step0c.pdb.2#</p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;">Wrote pdb files with previous and current coordinates</p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;"><br></p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;">-------------------------------------------------------</p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;">Program gmx_mpi, VERSION 5.0</p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;">Source code file: /share/gromacs-5.0/src/gromacs/mdlib/coupling.c, line: 1439</p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;"><br></p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;">Fatal error:</p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;">The v-rescale thermostat was called with a group with #DOF=2.999250, but for #DOF<3 only integer #DOF are supported</p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;">For more information and tips for troubleshooting, please check the GROMACS</p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;">website at http://www.gromacs.org/Documentation/Errors</p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;">-------------------------------------------------------</p><div><br></div><div><br></div><div><br></div><div><br></div><div>The SWM4-NDP file can be downloaded directly from virtualchemistry.org</div><div><br></div><p style="font-family: Gulim; font-size: 10pt; border: 0px; padding: 0px; margin: 0px; cursor: text;">Cheers, </p><p style="font-family: Gulim; font-size: 10pt; border: 0px; padding: 0px; margin: 0px; cursor: text;">Kester</p><div style="font-family: 돋움, arial; font-size: 12px; margin-top: 30px; margin-left: 0.8em; color: rgb(0, 102, 204); font-weight: bold;">--------- 원본 메일 ---------</div><blockquote style="font-family: Gulim; font-size: 12px; border-left-style: solid; border-left-width: 2px; margin: 0pt 0pt 0pt 0.8em; padding-left: 1em;"><div style="font-family:arial,돋움;line-height:1.5"><b>보낸사람</b> : Mark Abraham <mark.j.abraham@gmail.com><br><b>받는사람</b> : Discussion list for GROMACS us <gmx-users@gromacs.org><br><b>받은날짜</b> : 2014년 10월 10일(금) 21:35:03<br><b>제목</b> : Re: [gmx-users] v-rescale fatal error<br><!-- original content --><div style="margin-top:5px;"><pre>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 <kester2014@ibs.re.kr> 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 <jalemkul@vt.edu>
> *받는사람* : <gmx-users@gromacs.org>
> *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
>
> jalemkul@outerbanks.umaryland.edu | (410) 706-7441http://mackerell.umaryland.edu/~jalemkul
>
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</gmx-users@gromacs.org></jalemkul@vt.edu></kester2014@ibs.re.kr></pre></div><!-- original content --><br></div></blockquote></p>
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