[gmx-users] Converting Gromacs output files to dl_poly output files.
Mohammad Hossein Kowsari
mhkowsari2010 at gmail.com
Thu Feb 25 06:54:21 CET 2010
Thanks a lot for the files that you send.
I know the DL_POLY code create only site-site radial distribution
functions (g(r)) as an OUTPUT file named RDFDAT. Indeed, DL_POLY can
not create the Spatial Distribution Functions (SDFs) directly and I am
not familiar with any proposed program for converting of trajectory
file of DL_POLY (named HISTORY) to SDFs. However, several groups in
literature simulated their systems by DL_POLY and finally reported
SDFs, but you should know this code has not direct tools for this aim.
Generally people used of Tranal utility of MDynamix simulation code
(http://www.mmk.su.se/~sasha/mdynamix/) for make the SDFs and
afterwards, they visual this functions by gOpenMOL program. I think
that they used HISTORY file of DL_POLY as an INPUT for the MDynamix
simulation code. Thus,
I think that you can easier convert the trajectory file of GROMACS to
the SDFs and maybe, it is not needed using DL_POLY for your aim.
Finally, I can send an example input files of DL_POLY code for
imidazolium-based ILs for you if it needed!! However, I think you can
used of trajectory file of GROMACS code. Also, maybe GROMACS has any
tools (perhaps g_sdf) for calculating of SDFs and then you used of
gOpenMol for visualization.
If you send you question about calculating SDFs to gmx-mailing list, I
think you get better guidance for your problem.
Isfahan University of Technology
On 2/25/10, naimah haron naimah <cimot_ima98 at yahoo.com> wrote:
> Dear MH Kowsari,
> Actually, I want to calculate the spatial distribution function by using
> DL_POLY program. Now, I'm already run the simulation for 10 ns for my amino
> acid ionic liquids (AAILs). The output file that I get from GROMACS such as
> .tpr, and .trr. So now, I want to convert GROMACS ouput files (*.tpr and
> *.trr) to DL_POLY output (HISTORY,or file *.HISu, or file *.HISf). I attach
> the example of GROMACS input files ( *.itp and *.top) as your request...
> From: Mohammad Hossein Kowsari <mhkowsari2010 at gmail.com>
> To: gmx-users at gromacs.org
> Cc: naimah haron naimah <cimot_ima98 at yahoo.com>
> Sent: Wed, February 24, 2010 9:40:29 PM
> Subject: RE: [gmx-users] Converting Gromacs output files to dl_poly output
> Dear naimah,
> I have certainly inverse problem. I simulated several imidazolium-based ILs
> by DL_POLY code using of all- atom Canongia Lopes force field parameters
> (JPC B 2004); but now I like more study these liquids by GROMACS code.
> I think that you should firstly convert GROMACS input files (*.gro,
> *.top/*.itp, *.mdp) to DL_POLY input files (CONFIG, CONTROL, and FIELD).
> afterwards, you can start simulations with DL_POLY and get the OUTPUTs. what
> is the specific source of your OPLS_AA force field!. Is it from Lopes
> parameters?!. if I see your GROMACS input files of ILs , may be I can help
> you for constructing of DL_POLY file. by this order, may be my problem will
> be also solved because I start with GROMACS code now, while I worked by
> DL_POLY several years. I needed any help for convert IL input files of
> DL_POLY to GROMACS!
> Best Regards,
> MH Kowsari
> Isfahan University of Technology
> Message: 3
> Date: Tue, 23 Feb 2010 21:05:34 -0800 (PST)
> From: naimah haron naimah <cimot_ima98 at yahoo.com>
> Subject: [gmx-users] Converting Gromacs output files to dl_poly output
> To: gromacs <gmx-users at gromacs.org>
> Message-ID: <133636.25838.qm at web36507.mail.mud.yahoo.com>
> Content-Type: text/plain; charset="us-ascii"
> Dear Gromacs users,
> I simulated ionic liquids by GROMACS code. The force field that I used was
> Now, I like continuous my work on these ionic systems by DL_POLY code. Have
> anyone know the
> proper/simple way for converting GROMACS output files to DL_POLY output.
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