[gmx-users] Implicit solvent simulation

[Eric Jakobsson]

There is a niche for implicit solvent if you need to do more 
extensive conformational sampling than you can achieve with 
atomically detailed solvent---and if you can plausibly argue that you 
are not introducing such egregious systematic errors that you are 
just sampling more junk.

At 09:23 AM 7/18/2007, TJ Piggot wrote:
>If you REALLY want implicit solvent then i suggest you contact the 
>authors and ask them about it, however i (like most others i think) 
>have never needed to use implicit solvent.
>
>Tom
>
>--On Wednesday, July 18, 2007 16:17:01 +0200 Ran Friedman 
><r.friedman at bioc.unizh.ch> wrote:
>
>>Dear Tom,
>>
>>The paper is available and was mentioned in the list. The model,
>>however, isn't available AFAIK.
>>
>>Ran.
>>
>>TJ Piggot wrote:
>>>Hi,
>>>
>>>Just to let people know in case they are unaware there is a paper
>>>where implicit solvent models have been implemented in GROMACS, the
>>>paper can be found using the following link:
>>>
>>>http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid
>>>=15814616
>>>
>>>
>>>Tom
>>>
>>>--On Wednesday, July 18, 2007 15:39:43 +0200 David van der Spoel
>>><spoel at xray.bmc.uu.se> wrote:
>>>
>>>>SeungPyo Hong wrote:
>>>>>Thank you for your kind reply, Stephane.
>>>>>Anyhow it is a little disappointing that Generalized-Born is not
>>>>>implemented in Gromacs.
>>>>
>>>>I've put it on the development TODO list (feel free to volunteer)
>>>>
>>>>http://wiki.gromacs.org/index.php/Implicit_Solvent
>>>>
>>>>The reason it is not there is because none of the developers has
>>>>considered it worthwhile.
>>>>
>>>>--
>>>>David van der Spoel, Ph.D.
>>>>Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
>>>>Box 596, 75124 Uppsala, Sweden. Phone:    +46184714205. Fax:
>>>>+4618511755.
>>>>spoel at xray.bmc.uu.se    spoel at gromacs.org   http://folding.bmc.uu.se
>>>>_______________________________________________
>>>>gmx-users mailing list    gmx-users at gromacs.org
>>>>http://www.gromacs.org/mailman/listinfo/gmx-users
>>>>Please search the archive at http://www.gromacs.org/search before
>>>>posting!
>>>>Please don't post (un)subscribe requests to the list. Use the www
>>>>interface or send it to gmx-users-request at gromacs.org.
>>>>Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>>
>>>
>>>
>>>----------------------
>>>TJ Piggot
>>>t.piggot at bristol.ac.uk
>>>University of Bristol, UK.
>>>
>>>_______________________________________________
>>>gmx-users mailing list    gmx-users at gromacs.org
>>>http://www.gromacs.org/mailman/listinfo/gmx-users
>>>Please search the archive at http://www.gromacs.org/search before
>>>posting!
>>>Please don't post (un)subscribe requests to the list. Use the www
>>>interface or send it to gmx-users-request at gromacs.org.
>>>Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>>
>>--
>>------------------------------------------------------
>>Ran Friedman
>>Postdoctoral Fellow
>>Computational Structural Biology Group (A. Caflisch)
>>Department of Biochemistry
>>University of Zurich
>>Winterthurerstrasse 190
>>CH-8057 Zurich, Switzerland
>>Tel. +41-44-6355593
>>Email: r.friedman at bioc.unizh.ch
>>Skype: ran.friedman
>>------------------------------------------------------
>>
>>_______________________________________________
>>gmx-users mailing list    gmx-users at gromacs.org
>>http://www.gromacs.org/mailman/listinfo/gmx-users
>>Please search the archive at http://www.gromacs.org/search before posting!
>>Please don't post (un)subscribe requests to the list. Use the
>>www interface or send it to gmx-users-request at gromacs.org.
>>Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>
>
>----------------------
>TJ Piggot
>t.piggot at bristol.ac.uk
>University of Bristol, UK.
>
>_______________________________________________
>gmx-users mailing list    gmx-users at gromacs.org
>http://www.gromacs.org/mailman/listinfo/gmx-users
>Please search the archive at http://www.gromacs.org/search before posting!
>Please don't post (un)subscribe requests to the list. Use the www 
>interface or send it to gmx-users-request at gromacs.org.
>Can't post? Read http://www.gromacs.org/mailing_lists/users.php

---------------------------------
Eric Jakobsson, Ph.D.
Professor, Department of Molecular and Integrative Physiology, and of 
Biochemistry, and of the Center for Biophysics and Computational Biology
Senior Research Scientist, National Center for Supercomputing Applications
Professor, Beckman Institute for Advanced Science and Technology
3261 Beckman Institute, mc251
University of Illinois, Urbana, IL 61801
ph. 217-244-2896  Fax 217 244 9757