Dear Naimah, 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.
Best Regards, MH Kowsari Isfahan University of Technology On 2/25/10, naimah haron naimah <cimot_im...@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... > > Thanks > > Regards > > IMA > > > > ________________________________ > From: Mohammad Hossein Kowsari <mhkowsari2...@gmail.com> > To: gmx-users@gromacs.org > Cc: naimah haron naimah <cimot_im...@yahoo.com> > Sent: Wed, February 24, 2010 9:40:29 PM > Subject: RE: [gmx-users] Converting Gromacs output files to dl_poly output > files. > > > 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_im...@yahoo.com> > Subject: [gmx-users] Converting Gromacs output files to dl_poly output > files. > To: gromacs <gmx-users@gromacs.org> > Message-ID: <133636.25838...@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 > OPLS-AA. > 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. > Thanks > IMA > > > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
