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 <jalem...@vt.edu
<mailto:jalem...@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
<mitomas...@gmail.com <mailto:mitomas...@gmail.com>
<mailto:mitomas...@gmail.com <mailto:mitomas...@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 <priyankapanwa...@gmail.com
<mailto:priyankapanwa...@gmail.com>
<mailto:priyankapanwa...@gmail.com
<mailto:priyankapanwa...@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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