[gmx-users] Help for running gromacs

[Justin A. Lemkul]

What compilers did you use to install Gromacs?  Often times hangs and other 
memory errors are related to buggy compilers.

-Justin

priyanka panwar wrote:
> Command line was " genion -s em.tpr -o ions.pdb -np 4"
> 
> On Mon, May 3, 2010 at 5:19 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     priyanka panwar wrote:
> 
>         Hi,
>         Thanks for help.
>         -Command line was:
>         Number of (3-Atomic) solvent molecules:4256
>         Replacing solvent molecule 499 (atom 2784) with Na
> 
> 
>     That's not a command line.  What command did you actually type
>     (exactly) to run genion?
> 
> 
>         -Group selected was: 12 (SOL)
>         -Gromacs version I am using is 3.3.1
> 
> 
>     In the absence of any compelling reason (i.e., consistency with
>     previous simulations), using a Gromacs version that is four years
>     old is not recommended.  The new 4.0.x series is substantially
>     faster and has many new features.
> 
>     -Justin
> 
>         On Mon, May 3, 2010 at 4:31 PM, Krzysztof Mlynarczyk
>         <mitomaster at gmail.com <mailto:mitomaster at gmail.com>
>         <mailto:mitomaster at gmail.com <mailto:mitomaster at gmail.com>>> wrote:
> 
>            Please post more details including the following:
> 
>                * What is the exact command line?
>                * What group do you select as a "continuous solvent"? I
>         know it
>                  might sound weird to ask this but what I learned while
>                  teaching students is that these questions really should be
>                  asked when there are problems.
>                * Which version of Gromacs are you using?
> 
> 
>            2010/5/3 priyanka panwar <priyankapanwar20 at gmail.com
>         <mailto:priyankapanwar20 at gmail.com>
>            <mailto:priyankapanwar20 at gmail.com
>         <mailto:priyankapanwar20 at gmail.com>>>
> 
> 
>                I am  using Gromacs for Simulation of Insulin.I have
>         generated
>                most of the files but unable to generate the ions.pdb
>         file.The
>                system is becoming idle after the Selection command. A
>         line on
>                the command prompt appears as "replacing solvent molecule
>         with
>                Na" and remains as such for many hours. Is this step really
>                takes too much time or I am doing something wrong.      
>           Thanks
>                --
>                gmx-users mailing list    gmx-users at gromacs.org
>         <mailto:gmx-users at gromacs.org>
>                <mailto:gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>
> 
>                http://lists.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
>         <mailto:gmx-users-request at gromacs.org>
>                <mailto:gmx-users-request at gromacs.org
>         <mailto:gmx-users-request at gromacs.org>>.
> 
>                Can't post? Read
>         http://www.gromacs.org/mailing_lists/users.php
> 
> 
> 
>            --
>            gmx-users mailing list    gmx-users at gromacs.org
>         <mailto:gmx-users at gromacs.org>
>            <mailto:gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>
> 
>            http://lists.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
>         <mailto:gmx-users-request at gromacs.org>
>            <mailto:gmx-users-request at gromacs.org
>         <mailto:gmx-users-request at gromacs.org>>.
> 
>            Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> 
> 
> 
>     -- 
>     ========================================
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
>     ========================================
>     -- 
>     gmx-users mailing list    gmx-users at gromacs.org
>     <mailto:gmx-users at gromacs.org>
>     http://lists.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
>     <mailto:gmx-users-request at gromacs.org>.
>     Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> 
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================