[gmx-users] Converting Gromacs output files to dl_poly output files.

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] Query about g_hbond

Dear gmx-users... I am new to gromacs, I am trying to obtain the intermolecular hydrogen bonds formed during 10ns simulation of 125 ionic liquid (tetraethylammonium L-Lysinate). I use OPLS-AA force field for this simulation. When I do this by using g_hbond and selecting the LYS group, I am gett

[gmx-users] spatial distribution function for ionic liquid

Dear all... I want to get spatial distribution function for ionic liquid. So, I used g_sdf command as below g_sdf -f mixture_mdpr.trr -n index.ndx -s mixture_mdpr.tpr -o sdf_plt.dat -r sdf.gro -mode 1 -grid 3.8 3.8 3.8 I rename the output file from .dat file to .plt file and I used VMD to view

[gmx-users] spatial distribution function (SDF)

Hai all... Did anyone know how to do spatial distribution functions??? I have 125 ion pairs in my system. The problem is, 1)how I can I get the 3-D probability distributions of anion around cation or cation around anion in my system? Could anybody tell me the method? 2)When I read the GROMACS

[gmx-users] program to look at the coordination number

Hai All Did anyone know a program to look at the coordination number for molecules??? Thanks... IMA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please

[gmx-users] Re: how to calculate g_sdf and ionic conductivity

ode0 are more than a cell length out of the domain decomposition cell of their charge group (Mark Abraham) 6. g_rdf and number of atoms to include (Enemark Soeren) 7. how to calculate g_sdf and ionic conductivity (naimah haron naimah) 8. Re: how to calculate g_sdf a

[gmx-users] how to calculate g_sdf and ionic conductivity

Hello all Did anyone know how to 1) calculate g_sdf? 2) ionic conductivity? Can I have the commands for that Thanks IMA ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Pl

[gmx-users] replacing PRODRG charges with GAMESS charges

Dear all... I want to run a MD in an unparameterized molecule ionics liquids. I can get the approximated parameters in PRODRG. But I have read that PRODRG not always give the correct charge. Is it a good idea to replace that charges using the charges given with gamess software? The target forcefiel

[gmx-users] B3LYP/6-31++G** GAMESS derived charges to replace PRODRG assigned ones

Dear all... Can I replace the charges that I get from B3LYP/6-31++G** GAMESS derived with the original PRODRG charges? Is this the right way to proceed ? Thanks.. IMA ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org

[gmx-users] Height of the box

Dear all... How to obtain the height of the box after MD simulation finish? This is because, during simulation, I didn't put size of my box. The reason why I didn't put the size because I want put the molecule in random displacement to avoid bottlenecks. So the command is editconf -f cat125

[gmx-users] Interpretation of g_chi results

Dear All: I saw in the manual that by g_chi the NMR and Jcoupling of the system can be calculated. But when I perform the command which is  Then I got these 2 output file which is: g_chi -s cat125_md.gro -f cat125_md.xtc -o nmr.xvg -jc Jcoupling.xvg -shift   @ title "Dihedral Order Parameters

[gmx-users] how to get charge group number (cgnr)

Dear all... How to get charge group number(cgnr), if I want to construct my own topologies? Thank you for your suggestion and information...  Naimah Haron Graduate Research Assistant Department of Chemistry Universiti Putra Malaysia Malaysia _

[gmx-users] topology

Dear all... How to draw the structure for ionic liquid and get their PDB file? For example, we can draw the struture by using PRODRG generation server and get their PDB file. So, any suggestion to draw the structure and get their PDB file without using PRODRG generation server? Thank you for y

[gmx-users] ready topology for ionic liquid?

how do i get the ready topology for ionic liquid?? ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (

[gmx-users] help- ionic liquid

how to do molecular dynamics for ionic liquids by using GROMACS. Can u tell me the correct method to do molecular dynamics and which topologies are suitable for use with NMR-type calculations or all-atom force fields. ___ gmx-users mailing list

[gmx-users] email

[EMAIL PROTECTED] ___ gmx-users mailing listgmx-users@gromacs.org http://www.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

[gmx-users] ionic liquid

how to do molecular dynamics for ionic liquids by using GROMACS. Can u tell me the correct method to do molecular dynamics and which topologies are suitable for use with NMR-type calculations or all-atom force fields. ___ gmx-users mailing list