Dan is correct that the submissions are usually so specific that it
isn't easy to make a generic script. Things that change include job
schedulers (loadleveler? sun grid engine? torque? pbs?), specific job
requirements (overwrite? use reference coordinates?), and paths to
input and output files. That is, there really aren't any "typical" MD
jobs.
Is there something specific that you need to do and are having trouble with?
On Tue, Jun 17, 2014 at 2:16 PM, James Starlight <jmsstarlight.gmail.com> wrote:
> Hi Dan,
>
>
> many thanks for the bash guide- I've found it very useful. In general I'd
> like to look at some basic bash script examples suitable for typical md
> jobs dealing with the running of many of simulation on clusters because the
> most complicated examples like replica exchange simulation have already
> been present in the amber tutorials.
>
>
> James
>
>
> 2014-06-17 1:11 GMT+04:00 Daniel Roe <daniel.r.roe.gmail.com>:
>
>> Hi,
>>
>> On Mon, Jun 16, 2014 at 1:59 PM, James Starlight <jmsstarlight.gmail.com>
>> wrote:
>>
>> > Does someone know how would be possible to improve such scripts? Also
>> I'll
>> > be thankful for any other useful examples.
>> >
>>
>> The answer to this is going to depend completely on what you ultimately
>> want to accomplish. It appears that the scripts that you posted have very
>> specific goals, which may not ultimately be what you want to do.
>>
>> One resource I have found to be particularly useful is the 'Advanced Bash
>> Scripting Guide', http://www.tldp.org/LDP/abs/html/. It contains many
>> useful examples of bash scripting.
>>
>> Good luck,
>>
>> -Dan
>>
>>
>> >
>> >
>> > James
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>>
>>
>>
>> --
>> -------------------------
>> Daniel R. Roe, PhD
>> Department of Medicinal Chemistry
>> University of Utah
>> 30 South 2000 East, Room 201
>> Salt Lake City, UT 84112-5820
>> http://home.chpc.utah.edu/~cheatham/
>> (801) 587-9652
>> (801) 585-6208 (Fax)
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jun 17 2014 - 12:00:02 PDT
