Re: [gmx-users] Choosing water molecules and box type and dimensions

st? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Abhijit kayal Research Scholar Theoretical Chemistry IIT Kanpur -- Gromacs Us

Re: [gmx-users] Choosing water molecules and box type and dimensions

at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to

Re: [gmx-users] on the xmgrac for gromacs

://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Abhijit kayal Research Scholar Theoretical Chemistry IIT Kanpur -- Gromacs Users mailing list * Please

Re: [gmx-users] help on Graphene Nano Sheets

://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Abhijit

Re: [gmx-users] error in grompp if used TIP4p-Ew water at pdb2gmx

. Regards, Raja On Apr 16, 2015 4:10 PM, abhijit Kayal abhijitchemi...@gmail.com wrote: How did you solvate your system? What exact command did you use? On Thu, Apr 16, 2015 at 2:37 PM, Raj D gromacs.fo...@gmail.com wrote: Dear Users, I want to use TIP4P-Ew water model for my simulation

Re: [gmx-users] error in grompp if used TIP4p-Ew water at pdb2gmx

/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Abhijit kayal Research Scholar Theoretical Chemistry IIT Kanpur -- Gromacs Users mailing list * Please search the archive

Re: [gmx-users] Topology file for Fullerene with OPLS_AA force field

://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Abhijit

Re: [gmx-users] x2top segmentation fault in gromacs 5.0.x, but runs well for 4.0.x, 4.6.x

://www.dropbox.com/s/qv4j33sivn56iey/test_x2top.tgz?dl=0 I prepared the modified OPLS/AA force filed as described earlier in this list, post by Dr. Abhijit Kayal ( https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2014-July/090353.html ). A topology file can be generated by the g_x2top module

Re: [gmx-users] x2top segmentation fault in gromacs 5.0.x, but runs well for 4.0.x, 4.6.x

problematic ...) /ren -- Hao Ren, Ph. D. Center for Bioengineering Biotechnology China University of Petroleum Huangdao, Qingdao, Shandong 266580, P. R. China Email: r...@upc.edu.cn Tel: +86-(532) 8698 1135 http://pme.upc.edu.cn/~ren On Fri, Mar 27, 2015 at 8:27 PM, abhijit Kayal

[gmx-users] charge vibrating periodically

. So my question is how can I incorporate the vibrating charge in gromacs. In this paper they performed the simulations in gromacs. Any kind of help is highly appreciated. Here is the link of the paper: http://onlinelibrary.wiley.com/doi/10.1002/anie.201408633/abstract Thanks Abhijit -- Abhijit

[gmx-users] vibrating charge

. So my question is how can I incorporate the vibrating charge in gromacs. In this paper they performed the simulations in gromacs. Any kind of help is highly appreciated. Here is the link of the paper: http://onlinelibrary.wiley.com/doi/10.1002/anie.201408633/abstract Thanks Abhijit -- Abhijit

Re: [gmx-users] GROMPP COMMAND

/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Abhijit kayal Research Scholar

Re: [gmx-users] Graphene topology file

...@maillist.sys.kth.se on behalf of abhijit Kayal abhijitchemi...@gmail.com Sent: Friday, July 4, 2014 2:21 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Graphene topology file Hi Sukriti, Can you tell me the g_x2top command you have given and the grompp output. Thanks Abhijit

Re: [gmx-users] Graphene topology file

* For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Abhijit kayal Research Scholar Theoretical Chemistry IIT Kanpur -- Gromacs Users mailing list * Please search the archive at http

Re: [gmx-users] how to generate .top file

. -- Abhijit kayal Research Scholar Theoretical Chemistry IIT Kanpur -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe

Re: [gmx-users] (no subject)

Thanks Justin for the help. But if I want to look the dipole auto correlation or hydrogen bond dynamics ... is that possible? On Fri, Feb 28, 2014 at 4:38 PM, Justin Lemkul jalem...@vt.edu wrote: On 2/28/14, 5:38 AM, abhijit Kayal wrote: Dear Gromacs users, My system contained

Re: [gmx-users] CNT in water

)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Abhijit kayal Research Scholar Theoretical Chemistry IIT Kanpur -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org

Re: [gmx-users] RDF of Zn_water system using VMD/g_rdf

a mail to gmx-users-requ...@gromacs.org. -- Abhijit kayal Research Scholar Theoretical Chemistry IIT Kanpur -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org

Re: [gmx-users] radial distribution function of fullerene COM and O of water

-users or send a mail to gmx-users-requ...@gromacs.org. -- Abhijit kayal Research Scholar Theoretical Chemistry IIT Kanpur -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http