<p style="border:0; padding:0; margin:0; font-family:'Gulim'; font-size:10pt; cursor: text;"><p style="border:0; padding:0; margin:0; font-family:'Gulim'; font-size:10pt; cursor: text;">Hi Dr. Chaban, </p><p style="border:0; padding:0; margin:0; font-family:'Gulim'; font-size:10pt; cursor: text;"><br></p><p style="border:0; padding:0; margin:0; font-family:'Gulim'; font-size:10pt; cursor: text;">The four dummy atoms carry a mass of 1 a.m.u each, hence the oxygen mass of 11.998.</p><p style="border:0; padding:0; margin:0; font-family:'Gulim'; font-size:10pt; cursor: text;">However, what I don't understand is that the same atom has a mass of 0.0 under [ atomtypes ].</p><p style="border:0; padding:0; margin:0; font-family:'Gulim'; font-size:10pt; cursor: text;"><br></p><p style="border:0; padding:0; margin:0; font-family:'Gulim'; font-size:10pt; cursor: text;">For a system consisting of graphene, water and (Na+ OH-, or H3O+ Cl-) ions, if there is nonbonding-parameters specified, will having a different fudge value (0.5 instead of 1.0) make a difference?</p><p style="border:0; padding:0; margin:0; font-family:'Gulim'; font-size:10pt; cursor: text;"><br></p><p style="border:0; padding:0; margin:0; font-family:'Gulim'; font-size:10pt; cursor: text;">Thank you in advance.</p><p style="border:0; padding:0; margin:0; font-family:'Gulim'; font-size:10pt; cursor: text;"><br></p><p style="border:0; padding:0; margin:0; font-family:'Gulim'; font-size:10pt; cursor: text;">Regards,</p><p style="border:0; padding:0; margin:0; font-family:'Gulim'; font-size:10pt; cursor: text;">Kester</p><div style="margin-top:30px;margin-left:0.8em;font-size:12px;font-family:돋움,arial;color:#0066CC;font-weight: bold;">--------- 원본 메일 ---------</div><blockquote style="font-size:12px;border-left-style:solid;border-left-width:2px;margin-bottom:0pt;margin-left:0.8em;margin-right:0pt;margin-top:0pt;padding-left:1em;"><div style="font-family:arial,돋움;line-height:1.5"><b>보낸사람</b> : "Dr. Vitaly Chaban" <vvchaban@gmail.com><br><b>받는사람</b> : <gmx-users@gromacs.org><br><b>받은날짜</b> : 2014년 10월 18일(토) 16:20:49<br><b>제목</b> : Re: [gmx-users] SWM4-NDP force field<br><!-- original content --><div style="margin-top:5px;"><pre>The assigned masses are due to the presence of dummy atoms. The model
molecule must represent moments of inertia.
1-4 (fudgeLJ and fudgeQQ) interactions do not apply for water. So, you care
about a larger molecule only.
Dr. Vitaly V. Chaban
Виталий Витальевич ЧАБАН
On Sat, Oct 18, 2014 at 8:39 AM, Kester Wong <kester2014@ibs.re.kr> wrote:
>
> Dear all,
>
>
>
> I would like to know if this would cause a difference in MD calculations
(text highlighted in red):
>
> The assigned mass for the hydroxide O-atom seems to be inconsistent. Was
the zero atomic mass set with a specific purpose?
>
>
> #define SHELLPTYPE S
>
> #define SHELLMASS 0
>
> #define OXYGENMASS 15.9994
>
>
> [ atomtypes ]
>
> ; name btype mass charge ptype sigma epsilon
>
> SWM4-NDP_110a OD SHELLMASS -1.71636 SHELLPTYPE 0.0
0.0
>
> SWM4-NDP_OV1 OV1 1.0 0.0 A 0.24
0.294191
>
> SWM4-NDP_OV2 OV2 0.0 0.0 D 0.28
0.294191
>
> SWM4-NDP_H H 1.008 0.0 A 0.07
0.294191
>
> SWM4-NDP_qH qH 0.0 0.23 D 0.0 0.0
>
> <b>SWM4-NDP_O O 0.0 0.203 A 0.0 0.0</b>
>
>
>
> ; Hydroxide
>
> [ moleculetype ]
>
> ; molname nrexcl
>
> OH- 2
>
>
> [ atoms ]
>
> ; id at type res nr residu name at name cg nr charge mass
>
> 1 <b>SWM4-NDP_O 1 OH- O 1 0.202 11.998</b>
>
> 2 SWM4-NDP_110a 1 OH- OS 1 -1.432 0.00
>
> 3 SWM4-NDP_H 1 OH- H 1 0.00 1.008
>
> 4 SWM4-NDP_OV1 1 OH- OV1 1 0.00 1.0
>
> 5 SWM4-NDP_OV1 1 OH- OV1 1 0.00 1.0
>
> 6 SWM4-NDP_OV1 1 OH- OV1 1 0.00 1.0
>
> 7 SWM4-NDP_OV1 1 OH- OV1 1 0.00 1.0
>
> 8 SWM4-NDP_OV2 1 OH- OV2 1 0.00 0.00
>
> 9 SWM4-NDP_qH 1 OH- qH 1 0.23 0.00
>
>
> [ polarization ]
>
> #ifdef POL2WATER
>
> 1 2 2 0.0006809 0.02 16.736e8
>
> #else
>
> 1 2 1 0.0006809
>
> #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 0.0 418400
>
>
> [ constraints ]
>
> 3 1 1 0.0968
>
> 4 1 1 0.1463
>
> 5 1 1 0.1463
>
> 6 1 1 0.1463
>
> 7 1 1 0.1463
>
> 4 6 1 0.1979
>
> 6 5 1 0.1979
>
> 5 7 1 0.1979
>
> 7 4 1 0.1979
>
>
> #ifdef CONSTRAINTS
>
> [ constraints ]
>
> 3 4 1 0.15
>
> 3 5 1 0.15
>
> 3 6 1 0.15
>
> ; A fourth constraint would make the system redundant and therefore
>
> ; numerically unstable.
>
> ; 3 7 1 0.15
>
> #else
>
> [ angles ]
>
> 3 1 4 1 73.11 683
>
> 3 1 5 1 73.11 683
>
> 3 1 6 1 73.11 683
>
> 3 1 7 1 73.11 683
>
> #endif
>
>
> [ dummies2 ]
>
> 8 3 1 1 1.4390
>
> 9 3 1 1 -0.3099
>
>
> [ exclusions ]
>
> 1 2 3 4 5 6 7 8 9
>
> 2 1 3 4 5 6 7 8 9
>
> 3 1 2 4 5 6 7 8 9
>
> 4 1 2 3 5 6 7 8 9
>
> 5 1 2 3 4 6 7 8 9
>
> 6 1 2 3 4 5 7 8 9
>
> 7 1 2 3 4 5 6 8 9
>
> 8 1 2 3 4 5 6 7 9
>
> 9 1 2 3 4 5 6 7 8
>
>
>
> If I am to add/define graphene's bonded and nonbonded parameters into the
SWM4-NDP force field, using CHARMM27 parameters, should I take into
consideration the fudgeLJ and fudgeQQ differences (0.5 fudge LJ and fudgeQQ
in SWM4-NDP, 1.0 for fudgeLJ and fudgeQQ in CHARMM27)? The comb-rules are
the same (no.2).
>
>
>
> Thanks in advance!
>
> Kester
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</kester2014@ibs.re.kr></pre></div><!-- original content --><br></div></blockquote></p>
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