Re: [gmx-users] Regarding use of g_x2top utility in Gromacs

On 26/11/17 17:08, Rakesh Pant wrote: Dear Alex, But g-x2top doesn't work till we define all atom types in .n2t file. Please do not use this at all. Use acpype or something. Thanks On 26-Nov-2017 9:34 PM, "Alexandr Nasedkin" wrote: Hi, You will need to have both

Re: [gmx-users] Regarding use of g_x2top utility in Gromacs

Dear Alex, But g-x2top doesn't work till we define all atom types in .n2t file. Thanks On 26-Nov-2017 9:34 PM, "Alexandr Nasedkin" wrote: Hi, You will need to have both ffbonded.itp and ffnonbonded.itp . atomname2type.n2t is needed for g_x2top to make it work

Re: [gmx-users] Regarding use of g_x2top utility in Gromacs

Hi, You will need to have both ffbonded.itp and ffnonbonded.itp . atomname2type.n2t is needed for g_x2top to make it work correctly. Good luck. -Alex On 26/11/2017 10:52, Rakesh Pant wrote: Dear, Alex Does it mean, we do not need to define all the atomtypes in the .nt2 file. It is enough

Re: [gmx-users] Regarding use of g_x2top utility in Gromacs

Dear, Alex Does it mean, we do not need to define all the atomtypes in the .nt2 file. It is enough to define all types in bonded and non-bonded itp. Thanks, Rakesh Sent with Mailtrack

Re: [gmx-users] Regarding use of g_x2top utility in Gromacs

Edit the content of you ffnonbonded.itp file approximately this way: [ atomtypes ] ;name    at.num    mass        charge    ptype    sigma epsilon C    14    12.00    1.08    A    0.44000        0.63      ; OCE    8    15.999400    -0.70    A    0.35400        0.159705  ; C-O-C Bridging Oxygen;

Re: [gmx-users] Regarding use of g_x2top utility in Gromacs

Dear Alex, If I use O atoms to define the respective functional groups, then how to include the C atoms present in the molecule. Thanks, Rakesh Sent with Mailtrack On Sun, Nov

Re: [gmx-users] Regarding use of g_x2top utility in Gromacs

Hi, As I understood the problem, you need to distinguish between surface and buried carbons? You could define two atomtypes that differ in name and use it to process with x2top. Below is an example of *.n2t lines. You would need to change the charges and bondlengthes. ... O    OCH   

Re: [gmx-users] Regarding use of g_x2top utility in Gromacs

On 11/25/17 3:31 PM, Rakesh Pant wrote: But then I how will include the C atom (which is also one of the atomtypes)? No idea, but I know people on this list have dealt with graphene oxide before, so hopefully someone else chimes in. -Justin --

Re: [gmx-users] Regarding use of g_x2top utility in Gromacs

But then I how will include the C atom (which is also one of the atomtypes)? Thanks, Sent with Mailtrack On Sun, Nov 26, 2017 at 1:56 AM, Justin Lemkul wrote:

Re: [gmx-users] Regarding use of g_x2top utility in Gromacs

On 11/25/17 3:21 PM, Rakesh Pant wrote: Dear Justin, I am trying to use it for graphene oxide (layer), then what would be a better way if not g_x2top. Epoxide O and phenolic O have different connectivity (two C vs. one C and one H), so write the .n2t entries first based on O rather than C.

Re: [gmx-users] Regarding use of g_x2top utility in Gromacs

Dear Justin, I am trying to use it for graphene oxide (layer), then what would be a better way if not g_x2top. Thanks, Sent with Mailtrack On Sun, Nov 26, 2017 at 1:48 AM,

Re: [gmx-users] Regarding use of g_x2top utility in Gromacs

On 11/25/17 3:12 PM, Rakesh Pant wrote: Dear All, How does the utility g_x2top works? If we have similar connectivity in a molecule, then how will it read different atom types. Suppose a C atom is connected to 4 bonds (3 carbon atoms and 1 O atom, say in epoxy group) and similarly another C

[gmx-users] Regarding use of g_x2top utility in Gromacs

Dear All, How does the utility g_x2top works? If we have similar connectivity in a molecule, then how will it read different atom types. Suppose a C atom is connected to 4 bonds (3 carbon atoms and 1 O atom, say in epoxy group) and similarly another C atom is also connected to 4 atoms (3 C atoms