[gmx-users] constant pH simulations in GROMACS 4.5

[Antonio Baptista]

Hi,

Our PB/MC/MD approach to constant-pH simulations is implemented up to 
version 4.0.7 of GROMACS, but we don't currently have a usable 
distribution -- after using some collaborators as guinea pigs, we came to 
the conclusion that the current implementation is unintelligible, since no 
one besides those who wrote the scripts and are familiar with all the 
interfaced programs (GROMACS+MEAD+PETIT+etc) could actually use it... :-( 
We have already wrote a new and cleaner implementation which is being 
tested, so I hope we could finally make it available soon.

Best,
Antonio

-- 
Antonio M. Baptista
Instituto de Tecnologia Quimica e Biologica, Universidade Nova de Lisboa
Av. da Republica - EAN, 2780-157 Oeiras, Portugal
phone: +351-214469619         email: baptista at itqb.unl.pt
fax:   +351-214411277         WWW:   http://www.itqb.unl.pt/~baptista
--------------------------------------------------------------------------

On Thu, 22 Jan 2015, Gerrit Groenhof wrote:

> Hi,
>
> Our lamda-dynamics based approach works only in gromacs 3.3.3 at the moment.
>
> I don't know the status of the PB/MC/MD constant pH approach by Victorio Baptista and co-workers. Maybe that works in combination with gromacs 4.5, but he can tell you that.
>
> Best,
>
> Gerrit
>
>
>
> Message: 6
> Date: Thu, 22 Jan 2015 19:29:45 +0530
> From: Sahithya S Iyer <sah2714 at gmail.com>
> To: gmx-users at gromacs.org
> Subject: [gmx-users] constant pH simulations in GROMACS 4.5
> Message-ID:
> 	<CACPrdiQc9ufNboGcyM0n0xbVY7pFNDd4DZ0fVZN1-geVtCbycQ at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi users
> Have standard methods been developed in
> Gromacs
> 4.5 version to perform constant pH simulations ?
> -- 
> Sahithya
>
>
>
> Our methods so far only works in gromacs 3.3.3.
>
> I don't know the status of the constant pH approach by victorio baptista and co-workers. Maybe that works in combination with gromacs 4.5
>
> Best,
>
> Gerrit
>
>
>
> -- 
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
>