[gmx-users] Generate many random configurations
tsjerkw at gmail.com
Thu Mar 6 15:41:04 CET 2014
for ((i=0; i<$n; i++))
genbox ... -o tmp.gro
cat tmp.gro >> total.gro
That will not be slower, and it requires less disk space.
On Thu, Mar 6, 2014 at 2:29 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> On 3/6/14, 8:18 AM, rankinb wrote:
>> I have figured out to accomplish what I want by writing a bash script.
>> However, one thing I am still struggling with is determining how to
>> concatenate the resulting configurations. There are two possible
>> 1) concatenate multiple .gro files that have been generated at the end or
>> concatenate after each iteration. I like the idea of the second option.
>> Does anyone have any suggestions as to how to do this?
> I think option (1) would be much faster and cleaner, involving no
> intermediate files and cutting out a lot of steps. If you have conf.*.gro,
> where each has an index for the 1000 steps (e.g. conf.0.gro, conf.1.gro,
> ...), then a simple:
> cat `ls -rt conf.*.gro` > full.gro
> is all you need. With option (2), you have to do something like:
> if [ $i -eq 0 ]
> # do no concatenation
> mv conf.0.gro full.gro
> cat full.gro conf.$i.gro > tmp.gro
> rm full.gro
> mv tmp.gro full.gro
> The if-structure is within the loop and is executed every cycle. I
> imagine for 1000 iterations, that might slow down a fair bit, especially
> when full.gro starts to get large and you are using it in a concatenation
> step many times.
> Note that I haven't tested that script snippet, so don't just accept it
> blindly :)
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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Tsjerk A. Wassenaar, Ph.D.
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