[gmx-users] Fw: ionic liquids
-- Original Message -- From: prem...@iiserpune.ac.in To: vvcha...@gmail.com Date: Mon, 2 May 2011 11:29:44 +0530 (GMT+05:30) Subject: ionic liquids sir, I am grateful regarding your reply. The reported density for [bmim][bf4] system is 1.198 g/cm3.I was wondering whether you asked for the topology that I am using for my calculation or the one that Tsuzuki.et.al.(one I am referring) have used. Well, following is the toopology that I have created for my system. ; File 'bmim.top' was generated ; By user: onbekend (0) ; On host: onbekend ; At date: Fri Apr 15 18:03:14 2011 ; ; This is a include topology file ; ; It was generated using program: ; Generated by x2top ; ; Command line was: ; g_x2top_d -f boxbmim.pdb -o bmim.top ; ; Force field was read from the standard Gromacs share directory. ; ; Include forcefield parameters #include oplsaa.ff/forcefield.itp [ moleculetype ] ; Name nrexcl BIM 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 1 opls_557 1 BIM NA 1 0.24 14.0067 ; qtot 0.24 2 opls_560 1 BIM CW 2 -0.16 12.011 ; qtot 0.74 3 opls_561 1 BIM CW 3 -0.27 12.011 ; qtot 1.24 4 opls_557 1 BIM NA 4 0.32 14.0067 ; qtot 1.48 5 opls_558 1 BIM CR 5 -0.22 12.011 ; qtot 1.26 6 opls_905 1 BIM C1 6 -0.35 12.011 ; qtot 0.91 7 opls_908 1 BIM C1 7 -0.14 12.011 ; qtot 0.77 8 opls_136 1 BIM C2 8 -0.12 12.011 ; qtot 0.65 9 opls_136 1 BIM CS 9 -0.12 12.011 ; qtot 0.53 10 opls_135 1 BIM CT 10 -0.18 12.011 ; qtot 0.35 11 opls_565 1 BIM HA 2 0.23 1.008 ; qtot 0.41 12 opls_564 1 BIM HA 3 0.27 1.008 ; qtot 0.47 13 opls_563 1 BIM HA 5 0.25 1.008 ; qtot 0.53 14 opls_911 1 BIM H1 6 0.17 1.008 ; qtot 0.59 15 opls_911 1 BIM H1 6 0.17 1.008 ; qtot 0.65 16 opls_911 1 BIM H1 6 0.17 1.008 ; qtot 0.71 17 opls_911 1 BIM H1 7 0.16 1.008 ; qtot 0.77 18 opls_911 1 BIM H1 7 0.16 1.008 ; qtot 0.83 19 opls_140 1 BIM HC 8 0.06 1.008 ; qtot 0.89 20 opls_140 1 BIM HC 8 0.06 1.008 ; qtot 0.95 21 opls_140 1 BIM HC 9 0.06 1.008 ; qtot 1.01 22 opls_140 1 BIM HC 9 0.06 1.008 ; qtot 1.07 23 opls_140 1 BIM HC 10 0.06 1.008 ; qtot 1.13 24 opls_140 1 BIM HC 10 0.06 1.008 ; qtot 1.19 25 opls_140 1 BIM HC 10 0.06 1.008 ; qtot 1.25 [ bonds ] ; ai aj funct c0 c1 c2 c3 1 2 1 0.1372 178656.8 1 5 1 0.1340 199576.8 1 6 1 0.1466 141000.8 2 3 1 0.1375 217568.0 2 11 1 0.1080 138490.4 3 4 1 0.1372 178656.8 3 12 1 0.1080 138490.4 4 5 1 0.1340 199576.8 4 7 1 0.1466 141000.8 5 13 1 0.1080 138490.4 6 14 1 0.1090 138490.4
[gmx-users] Fw: ionic liquids
-- Original Message -- From: prem...@iiserpune.ac.in To: gmx-users@gromacs.org Date: Sat, 30 Apr 2011 10:30:53 +0530 (GMT+05:30) Subject: ionic liquids Sir, I am trying to create an ionic-liquid system comprising of 1-butyl-3-methyl-imidazolium(bmim) as cation and BF4-(bf4) as anion. I have generated the system using following command: genbox_d -cp bmim.gro -ci bf4.gro -nmol 125 -try 200 -o .pdb , well it created system of total 250 molecules 125 each but after equilibration the density is not matching with the reported.I tried simulated annealing procedure still no much difference. I wonder if there is any other way to generate an ionic liquid system or how the people do it tp reproduce the results , I urge for any quick suggestion. thanx, student. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Fw: ionic liquids
On 4/30/2011 5:20 PM, Prema Awati wrote: */-- Original Message --/* From: prem...@iiserpune.ac.in To: gmx-users@gromacs.org Date: Sat, 30 Apr 2011 10:30:53 +0530 (GMT+05:30) Subject: ionic liquids Sir, I am trying to create an ionic-liquid system comprising of 1-butyl-3-methyl-imidazolium(bmim) as cation and BF4-(bf4) as anion. I have generated the system using following command: genbox_d -cp bmim.gro -ci bf4.gro -nmol 125 -try 200 -o .pdb , well it created system of total 250 molecules 125 each but after equilibration the density is not matching with the reported.I tried simulated annealing procedure still no much difference. I wonder if there is any other way to generate an ionic liquid system or how the people do it tp reproduce the results , I urge for any quick suggestion. thanx, student. You can try to adapt the procedure here http://www.gromacs.org/Documentation/How-tos/Non-Water_Solvation Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
