[gmx-users] How to rolled up a polymer chain

of the force field that i choose i get :that Residue LIG not found. How to solve this? thanks MARCELLO CAMMARATA Ing., Ph.D., 3208790796 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before

[gmx-users] I: How to rolled up a polymer chain

with Gromacs, - in Cygwin it doen't work, i got a bash comand - the topology need a lig parameters. one more time, below there is my post. I wpould like if you can help me to solve this question, instead i can try to use an othere MD software. MARCELLO CAMMARATA Ing., Ph.D., 3208790796 Il Lunedì 22

Re: [gmx-users] I: How to rolled up a polymer chain

. but each time it ask me for the LIG. I have a bdp file with the chain, made by me. MARCELLO CAMMARATA Ing., Ph.D., 3208790796 Il Martedì 23 Settembre 2014 18:25, Mohd Farid Ismail mohd.farid.ism...@yandex.com ha scritto: Can I ask you something. What do you mean by rolled up? Do you

Re: [gmx-users] I: How to rolled up a polymer chain

? bests MARCELLO CAMMARATA Ing., Ph.D., 3208790796 Il Mercoledì 24 Settembre 2014 0:41, Johnny Lu johnny.lu...@gmail.com ha scritto: Molecular dynamics software, like gromacs, use a set of rules to simulate the real world. This set of rules is a force-field. Force field is the simplified

Re: [gmx-users] I: How to rolled up a polymer chain

database, aminoacid.r2b Questions are: how i can do for load that residue? What do you suggest to do for induce the software to load my residue? Bests. MARCELLO CAMMARATA Ing., Ph.D., 3208790796 Il Mercoledì 24 Settembre 2014 3:45, Mohd Farid Ismail mohd.farid.ism...@yandex.com ha scritto

[gmx-users] installation and running gromacs on windows

pdb2gmx: command not found so, i tryed to follow other advices in some blogs, also to set a path in the enviroment variables of the computer, but anything was changed. MARCELLO CAMMARATA Ing., Ph.D., 3208790796 -- Gromacs Users mailing list * Please search the archive at http

[gmx-users] question about topologies

Hi, i am studied the capter 5 about topology, and o did not understand some aspect: 1-in the a.tp file, what does means the number after the simbol? 0 15.999 (C==0) OM 15.99 (CO) C 12.01 (C=0, C-N) 2- witch differences are between O and C? 3- The file with the virtual sites what

[gmx-users] help on Graphene Nano Sheets

directive./* * Thanks Il 23/04/2015 14:35, Marcello Cammarata ha scritto: i unistalled GRO 5 and installed GRO4.6.7_ i run the x2top and i got this message:/ //Opening force field file /usr/local/gromacs/share/gromacs/top/cnt_oplsaa.ff/atomname2type.n2t// //There are 32 name to type translations

[gmx-users] help on Graphene Nano Sheets

and dihedrals from bonds... segmentazion fault (core dump created) Someone can help me on this? The graphene force field for nanolayer is the same for nanotube? There is something that i have to change? bests -- Marcello Cammarata, Ph.D. 3208790796 -- Gromacs Users mailing list * Please search

[gmx-users] help on Graphene Nano Sheets

https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Marcello Cammarata, Ph.D. 3208790796 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting

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

segmentazion fault (core dump created) MC Someone can help me on this? MC The graphene force field for nanolayer is the same for nanotube? There MC is something that i have to change? MC bests MC -- MC Marcello Cammarata, Ph.D. MC 3208790796 -- Marcello Cammarata, Ph.D. 3208790796 -- Gromacs

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

the latest version. Am I doing something wrong? :) On Wed, Apr 22, 2015 at 5:26 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/22/15 7:22 PM, marcello cammarata wrote: yes, i used the Minoia tutorial, i use a cnt_oplsaa at the first attempt, and forward i copied and modify the standard oplsaa folder

[gmx-users] help on Graphene Nano Sheets

to gmx-users-requ...@gromacs.org. MC -- MC Marcello Cammarata, Ph.D. MC 3208790796 -- Marcello Cammarata, Ph.D. 3208790796 -- 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