[gmx-users] Help for running gromacs
Justin A. Lemkul
jalemkul at vt.edu
Mon May 3 15:09:48 CEST 2010
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
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> --
> ========================================
>
> 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
>
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--
========================================
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
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