On 4/23/15 4:24 AM, Marcello Cammarata wrote:
Thanks Justin, and thanks Alex.
If i have run the command x2top using pbd file but i got the same error.
which files have i substitute to my version ( Gro5.0) with the ones from the
pre-5 version?
The command is the same; if you're getting a seg fault in 5.0.4 you need to use
version 4.6.7.
-Justin
Alex did you change something in your version? i am in ubuntu OS.
/GROMACS: gmx x2top, VERSION 5.0.4//
//Executable: /usr/local/gromacs/bin/gmx//
//Library dir: /usr/local/gromacs/share/gromacs/top//
//Command line://
// g_x2top -f Graphene15x15.pdb -o cnt.top -ff cnt2_oplsaa//
//
//WARNING: all CONECT records are ignored//
//Opening force field file
/usr/local/gromacs/share/gromacs/top/cnt2_oplsaa.ff/atomnames2types.n2t//
//Opening force field file
/usr/local/gromacs/share/gromacs/top/cnt2_oplsaa.ff/name_topology.n2t//
//There are 12 name to type translations in file cnt2_oplsaa.ff//
//Generating bonds from distances...//
//atom 112//
//There are 1 different atom types in your sample//
//Generating angles and dihedrals from bonds...//
//segmentation fauld (core dump created)/
if i want run the pdb file what command need i use? the same "x2top"? could it
work?
Il 23/04/2015 01:28, Alex ha scritto:
Justin, everything works for me with graphene/x2top under the latest
version. Am I doing something wrong? :)
On Wed, Apr 22, 2015 at 5:26 PM, Justin Lemkul <[email protected]> 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. with both of them i have the same trouble.
The seg fault will always occur with version 5.0.4; there is a bug we
discovered a few weeks back:
http://redmine.gromacs.org/issues/1711
You'll need to use an older version (pre-5.0) for x2top to work properly
(or patch the code and upload a fix to solve the bug :).
The inizial graphene layer was created using*VMD modelling toolbox*,
that was
a .pdb file, i convert it in .gro file using *editconf *command.
i open the gro file using Avogadro, and it is still a layer. But in the
gro file
the connections are loose.
CONECT entries in PDB files are rarely (never?) used in GROMACS. They are
totally irrelevant for the purpose of x2top.
-Justin
here i report the firt 5 rows of the graphene.gro file.
UNNAMED
112
1GRA C 1 0.000 0.000 0.000
2GRA C 2 -0.123 0.071 0.000
3GRA C 3 -0.123 0.213 0.000
4GRA C 4 0.000 0.284 0.000
5GRA C 5 0.246 0.000 0.000
thanks
Il 22/04/2015 19:46, Alex ha scritto:
Hello,
The forcefields for CNT and graphene are identical (for the purpose of
this discussion). Two questions:
1. Where did you get the initial graphene structure?
2. Are there any CONECT statements in it?
I assume you used Andrea Minoia's guide and the contents of your
cnt2_oplsaa.ff directory correspond to what he's got.
Alex
MC> Hi,
MC> i am trying to model a Graphene nano sheet GNS on Gromacs-
MC> I follow the advices about the nanotubes presented in the help site.
MC> _http://www.gromacs.org/Documentation/How-tos/Carbon_Nanotube_
MC> I run this command to greate the topology:
MC> _g_x2top -f graphene.gro -o cnt.top -ff cnt2_oplsaa_
MC> I got this error message:
MC> GROMACS: gmx x2top, VERSION 5.0.4
MC> Executable: /usr/local/gromacs/bin/gmx
MC> Library dir: /usr/local/gromacs/share/gromacs/top
MC> Command line:
MC> g_x2top -f graphene.gro -o cnt.top -ff cnt2_oplsaa
MC> Opening force field file
MC>
/usr/local/gromacs/share/gromacs/top/cnt2_oplsaa.ff/atomnames2types.n2t
MC> Opening force field file
MC> /usr/local/gromacs/share/gromacs/top/cnt2_oplsaa.ff/name_topology.n2t
MC> There are 12 name to type translations in file cnt2_oplsaa.ff
MC> Generating bonds from distances...
MC> atom 112
MC> There are 1 different atom types in your sample
MC> Generating angles and dihedrals from bonds...
MC> 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
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
[email protected] | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
--
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 requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
send a mail to [email protected].
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
[email protected] | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
--
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 requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
mail to [email protected].
