Re: [AMBER] Forcefield for RNA

From: koushik <>
Date: Thu, 23 Oct 2014 17:03:54 -0400

On Hai's comment on "converting to netcdf file again using cpptraj seems
very slow". Writing the trajectories directly to the current working
directory slows down the writing process because all the programs are
simultaneously accessing almost the same disk area. This is an even
bigger problem if you are extracting temperature trajectories from
multiple simulations, which is usually the case, at the same time.

If the script we are running is I/O intensive, its a really good
practice to copy the data to the storage space on local node, change to
the local node directory, execute the script, and copy back the files.
The following links explains this process.

The /cavern uses the Lustre file system. The link 3 above briefly
summarizes scratch data handling on Lustre file system.

To share my experience, I was writing the temperature trajectories from
56 REMD simulations on Laufer cluster and it took almost 10 hours for
all the jobs to finish (this also slowed down the jobs of others).
When I used the TMPDIR feature and ran the same number of scripts
submitting all at the same time, all of them finished within 15 minutes.

Another observation regarding Netcdf is that, if you use the "go" word
on line 6 of the code below, the writing speed of netcdf is really slow.
I have observed that cpptraj writes the Netcdf file twice if you use the
"go" word. When I ran the script without the "go" keyword below, it runs
fast. The "go" word is in a lot of analysis scripts on the wiki, hence,
if you are using the "go" keyword in your scripts, it slows down the
process of writing.

     TEMPLIST=`cat remd/temperatures.dat`
     for T in $TEMPLIST; do
     /cavern/koushik/amber2013-02-15/bin/cpptraj <<EOF
     trajin remd/trj/remd.trj.001 remdtraj remdtrajtemp $T
     trajout remd/temptraj/remd.Ttraj.$T netcdf


On 10/23/2014 04:58 PM, Jiri Sponer wrote:
> For RNA, you need to have chiOL3, to prevent spurious ladder-like
> structure. For RNA it is even more important than bsc0.
> alpha/gamma bsc0 is intended to prevent loss of DNA structure.
> chi chiOL3 is intended to prevent loss of RNA structure.
> You really need to READ first, before simulating.
> Jiri
> On Thu, 23 Oct 2014, Asfa Ali wrote:
>> Date: Thu, 23 Oct 2014 16:56:48 +0530
>> From: Asfa Ali <>
>> Reply-To: AMBER Mailing List <>
>> To: AMBER Mailing List <>
>> Subject: Re: [AMBER] Forcefield for RNA
>> Thank you so much for the above suggestions.
>> I have tried the following:
>> tleap -s -f leaprc.ff99bsc0
>> loadoff RNA_CI.lib
>> source leaprc.gaff
>> ....
>> and carried out the initial file preparation. There was no error/problem as
>> the structures after simulation runs were looking fine. So is the above
>> fine?
>> Also, as advised by Jiri Sponer, I didn't try chiOL3 along with ff99bsc0.
>> If I have to do so, should I load both the force fields simultaneously?
>> On Thu, Oct 23, 2014 at 4:37 PM, Jason Swails <>
>> wrote:
>>> On Thu, 2014-10-23 at 11:22 +0530, Asfa Ali wrote:
>>>> Hi all,
>>>> I wanted to know whether the forcefield ff99bsc0 suitable for RNA
>>>> simulations? Or is ff99SB better?
>>> In addition to advice you have already received, I suggest you look at
>>> the third chapter of the AmberTools manual, which has a lengthy
>>> discussion on force field choices in Amber (along with a set of
>>> references for further study if needed).
>>> HTH,
>>> Jason
>>> --
>>> Jason M. Swails
>>> BioMaPS,
>>> Rutgers University
>>> Postdoctoral Researcher
>>> _______________________________________________
>>> AMBER mailing list
>> --
>> Asfa Ali
>> Prof. S. Bhattacharya's group,
>> Dept. of Organic Chemistry,
>> Indian Institute of Science,
>> Bangalore-12
>> _______________________________________________
>> AMBER mailing list
> _______________________________________________
> AMBER mailing list

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Received on Thu Oct 23 2014 - 14:30:03 PDT
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