<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;">Dear Justin, </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 for the feedback. Yep, the converted structure is not any better than a starting configuration, i.e. discontinued ensemble velocitites and another energy minimisation for the converted structure is necessary.</p><p style="border:0; padding:0; margin:0; font-family:'Gulim'; font-size:10pt; cursor: text;">What I thought would be helpful is that for water droplet formation, users might save a couple of nanoseconds by having a droplet starting file, instead of a water box. </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;"><br></p><p style="border:0; padding:0; margin:0; font-family:'Gulim'; font-size:10pt; cursor: text;">Cheers, </p><p style="border:0; padding:0; margin:0; font-family:'Gulim'; font-size:10pt; cursor: text;"><span style="font-size: 10pt;">Kester</span></p><p style="border:0; padding:0; margin:0; font-family:'Gulim'; font-size:10pt; cursor: text;"><br></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> : Justin Lemkul <jalemkul@vt.edu><br><b>받는사람</b> : <gmx-users@gromacs.org><br><b>받은날짜</b> : 2014년 9월 17일(수) 02:29:13<br><b>제목</b> : Re: [gmx-users] Converting TIPS3P model to SWM4-NDP model<br><!-- original content --><div style="margin-top:5px;"><pre>
On 9/16/14 4:48 AM, Kester Wong wrote:
> Dear gromacs team,
>
>
> I have recently converted a TIPS3P system (10k molecules) to a SWM4-NDP model.
>
>
> As I followed the instruction as listed below, I find it hard for beginners like
> me to convert the water structure:
>
> http://www.gromacs.org/Documentation/How-tos/Changing_a_3_Point_Water_Model_to_a_4_Point_Water_Model
>
>
> Notwithstanding, after doing some reading and tinkering on the .gro file
> formatting, and tinkering, I have managed to convert TIPS3P water to SWM4-NDP
> models. I find this technique very useful, as I think I could probably save some
> computing time by having the first few ns of the equilibration of SWM4-NDP model
> done in a less expensive way (e.g. 3-point water model). It can be applied for
> other water models too, e.g. TIP3P to TIP4P and TIP5P conversions.
>
I don't know that there's much to gain by doing such conversions. You still
have to re-equilibrate no matter what, and the choice of TIP3P-equilibrated
configuration is arbitrary; the final configuration of the simulation is not
necessarily any better than any other snapshot, and you lose any semblance of
continuity because you can't preserve the equilibrated ensemble of velocities, etc.
-Justin
>
> I have devised a short step-by-step note that I think might be useful to other
> gromacs users. This could also be a good opportunity to update the web page with
> more information?
>
>
> Please let me know if this is okay, and I will send the notes as a doc. attachment?
>
>
> Regards,
>
> Kester
>
>
>
>
>
>
>
--
==================================================
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) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
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