[gmx-users] Help for running gromacs
priyanka panwar
priyankapanwar20 at gmail.com
Mon May 3 15:14:51 CEST 2010
I will download latest version of gromacs and start working with it.I will
be back if any face any problem. Thanks to all
On Mon, May 3, 2010 at 6:39 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
> 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/searchbefore
>> 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
>
> ========================================
> --
> gmx-users mailing list 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.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100503/3ca24341/attachment.html>
More information about the gromacs.org_gmx-users
mailing list