Re: [gmx-users] Graphene Sheet in GROMOS 54A7

many thanks for your reply :) I have the graphene sheet topology file .itp not .top. I am trying to evaporate some molecules on the graphene sheet. Unfortunately, I didn't find information in the manual about how to do such an evaporation on the graphene sheet. what I have now is the graphene

Re: [gmx-users] Graphene Sheet in GROMOS 54A7

Hi, What .itp file you have .. On Tue 4 Feb, 2020, 4:44 PM Mohamed Abdelaal, wrote: > Hello everybody :) > > I want to know how to simulate a graphene sheet in GROMOS 54A7 and get the > .top file knowing that I have the .itp file. > > Thanks > Mohamed > -- > Gromacs Users mailing list > > *

Re: [gmx-users] Graphene Sheet in GROMOS 54A7

http://manual.gromacs.org/2020/reference-manual/topologies/topology-file-formats.html?highlight=itp#molecule-itp-file There is an example there of how you include an itp within a top On Tue, 4 Feb. 2020, 10:13 pm Mohamed Abdelaal, wrote: > Hello everybody :) > > I want to know how to simulate

[gmx-users] Graphene Sheet in GROMOS 54A7

Hello everybody :) I want to know how to simulate a graphene sheet in GROMOS 54A7 and get the .top file knowing that I have the .itp file. Thanks Mohamed -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! *

Re: [gmx-users] Graphene sheet topology

Did you try googling "gromacs graphene topology" or "gromacs cnt topology"? To refine the interactions in existing tutorials, I actually wrote a paper a while back: http://iopscience.iop.org/article/10.1088/0957-4484/25/48/485701/meta -- which noone seems to cite. :) Improper dihedrals are

[gmx-users] Graphene sheet topology

Hi, Does anyone know how to build a graphene topology based on OPLS-AA force field? Also is it possible to let me know how can I determine the improper dihedral of graphene because graphene sheet has a lot of dihedrals and it is difficult for do that manually? -- Best Regards, Mostafa

Re: [gmx-users] Graphene simulation, regarding

Dear Alex Thank you On Tue, 20 Feb 2018 at 1:59 PM, Alex wrote: > This requires custom work, if you are determined to use Gromacs. > > If you actually read Andrea's full tutorial > (http://chembytes.wikidot.com/grocnt), it fully describes the basic > concept, so then it is

Re: [gmx-users] Graphene simulation, regarding

This requires custom work, if you are determined to use Gromacs. If you actually read Andrea's full tutorial (http://chembytes.wikidot.com/grocnt), it fully describes the basic concept, so then it is fairly clear how to proceed preparing files for x2top and then using it. For reduced GO you

[gmx-users] Graphene simulation, regarding

Dear all, Greetings. I want to perform a simulation of bilayer reduced graphene oxide in opls ff. The difficulty is to generate the topology file for the bilayer graphene oxide. Andrea Minoia's tutorial gives information only about the planar graphene sheets and nanotubes. How can I develop a

[gmx-users] graphene wall piston acceleration simulation

Dear Gromacs-User, I have a question regarding graphene wall piston simulation. As far as I understand, a constant acceleration/force is applied onto the graphene wall at x direction when I put acceleration = 0.1 0.0 0.0 . However when I look at the movie, it seems to have sudden jerk movement

[gmx-users] Graphene

Hi, I simulated the graphene by using this link "http://www.gromacs.org/Documentation/How-tos/Carbon_Nanotube;. Then, I solvated it in water using 'gmx solvate' command. But, when I wanted to add ions in the media by using 'gmx grompp' command, I got this error:...ERROR 6383 [file

Re: [gmx-users] Graphene modeling

Hi Justin, Thank you very much. It is Ok now. Best,Mohammad From: Justin Lemkul <jalem...@vt.edu> To: Discussion list for GROMACS users <gmx-us...@gromacs.org> Sent: Tuesday, 16 May 2017, 18:34:14 Subject: Re: [gmx-users] Graphene modeling On 5/16/17 7:31 AM, ‪Mohamm

Re: [gmx-users] Graphene modeling

ssary here. -Justin Best Mohammad *From:* ‪Mohammad Roostaie‬ ‪ <mohammad.r0...@yahoo.com> *To:* Justin Lemkul <jalem...@vt.edu>; gmx-us...@gromacs.org *Sent:* Tuesday, 16 May 2017, 13:59:29 *Subject:* Re

Re: [gmx-users] Graphene modeling

here are 1 different atom types in your sampleGenerating angles and dihedrals from bonds...Segmentation fault BestMohammad  From: ‪Mohammad Roostaie‬ ‪ <mohammad.r0...@yahoo.com> To: Justin Lemkul <jalem...@vt.edu>; gmx-us...@gromacs.org Sent: Tuesday, 16 May 2017, 13:59:29 S

Re: [gmx-users] Graphene modeling

0.00 12.011 3C 0.142 C 0.142 C 0.142 ;Internal/periodic C Thanks,Mohammad From: Justin Lemkul <jalem...@vt.edu> To: gmx-us...@gromacs.org; ‪Mohammad Roostaie‬ ‪ <mohammad.r0...@yahoo.com> Sent: Monday, 15 May 2017, 16:45:19 Subject: Re: [gmx-users] Graph

Re: [gmx-users] Graphene modeling

On 5/14/17 9:43 AM, ‪Mohammad Roostaie‬ ‪ wrote: Hi GROMACS users, I want to model a graphene sheet. I used the instruction stated in link http://www.gromacs.org/Documentation/How-tos/Carbon_Nanotube. I put the cnt_oplsaa.ff folder in the directory where I want to run the rest of the

[gmx-users] Graphene modeling

Hi GROMACS users,   I want to model a graphene sheet. I used the instruction stated in link http://www.gromacs.org/Documentation/How-tos/Carbon_Nanotube. I put the cnt_oplsaa.ff folder in the directory where I want to run the rest of the work. Also, I rename the residues of the graphene to

Re: [gmx-users] Graphene sheet topology

Thanks Justin as always for your prompt reply. I have now created the graphene topology the way u suggested that is I issued the following command 1. g_x2top -f file.gro -o graphene.top -pbc: I did not prefer to use the -noparam option since it does not print the k0, k1 and similar values. 2. I

Re: [gmx-users] Graphene sheet topology

On 4/23/16 1:37 AM, soumadwip ghosh wrote: Hello all, I am currently working on the interaction between a flat graphene sheet and nucleic acids at various physiological conditions. I am using CHARMM 27 force field and GROMACS 4.5.6 for MD simulations. Here is my work order 1. I

Re: [gmx-users] Graphene sheet topology

Hello all, I am currently working on the interaction between a flat graphene sheet and nucleic acids at various physiological conditions. I am using CHARMM 27 force field and GROMACS 4.5.6 for MD simulations. Here is my work order 1. I created a graphene.top file according to the

[gmx-users] Graphene sheet topology

Hello all, I am currently working on the interaction between a flat graphene sheet and nucleic acids at various physiological conditions. I am using CHARMM 27 force field and GROMACS 4.5.6 for MD simulations. Here is my work order 1. I created a graphene.top file according to the

[gmx-users] graphene top file

Dear gmx-users I built a graphene sheet (graphene.pdb ) by VMD. I convert it to gro file with editconf command. Then I made top file with g_x2top command. But in top file connection between atoms is not correct(highlighted lines below). How can I solve this problem? Connection in pdb file for

Re: [gmx-users] graphene top file

On 10/27/14 2:21 PM, fatemeh ramezani wrote: Dear gmx-users I built a graphene sheet (graphene.pdb ) by VMD. I convert it to gro file with editconf command. Then I made top file with g_x2top command. But in top file connection between atoms is not correct(highlighted lines below). How can I

Re: [gmx-users] Graphene topology file

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Justin Lemkul jalem...@vt.edu Sent: Thursday, July 17, 2014 7:50 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Graphene topology file On 7/17/14, 7:16 AM

Re: [gmx-users] Graphene topology file

On Mon, Aug 4, 2014 at 8:38 AM, #SUKRITI GUPTA# sukriti...@e.ntu.edu.sg wrote: Hi gromacs users, I was able to simulate graphene sheet in water. Now I want to simulate functionalised graphene sheet with -OH groups attached randomly to graphene sheet. I modified atomname2type.n2t file by

Re: [gmx-users] Graphene topology file

, 2014 11:20 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Graphene topology file Dear Justin, Thanks so much for your help. I am still unable to solve the problem of blowing up of the box. Once I am able to do correct simulation I will update here. Regards Sukriti Sukriti Gupta (Ms

Re: [gmx-users] Graphene topology file

On 7/17/14, 7:16 AM, #SUKRITI GUPTA# wrote: Hi gromacs users, I read that for slab geometries where you need pbc in xy, you can use pbc=xyz and have a slab of vacuum in between the periodic images in z and use ewald3dc (Yeh and Berkowitz method). So I changed my mdp file extended my box in

Re: [gmx-users] Graphene topology file

of Justin Lemkul jalem...@vt.edu Sent: Saturday, July 12, 2014 5:17 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Graphene topology file On 7/11/14, 5:42 AM, #SUKRITI GUPTA# wrote: Hi Justin, Thanks for the reply. I changed define= -dflexible to -dposres_water and removed freeze graphene

Re: [gmx-users] Graphene topology file

...@vt.edu Sent: Thursday, July 10, 2014 8:50 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Graphene topology file On 7/10/14, 8:46 AM, #SUKRITI GUPTA# wrote: Hi Justin, Thanks for the reply. Following is my npt.mdp file for pbc in xy direction: title = example cpp

Re: [gmx-users] Graphene topology file

On 7/11/14, 5:42 AM, #SUKRITI GUPTA# wrote: Hi Justin, Thanks for the reply. I changed define= -dflexible to -dposres_water and removed freeze graphene group in my .mdp file and ran the energy minimization and npt again. This time for pbc= xyz, the water doesn't fly away but the graphene

Re: [gmx-users] Graphene topology file

On 7/10/14, 1:29 AM, #SUKRITI GUPTA# wrote: Hi Justin, I did simulation 2 times, once with PBC in xy with walls and other time with pbc in xyz. For pbc in xy with walls with following wall parameters: nwall = 2 wall_type = 12-6 wall_density = 5 5 wall_atomtype = opls_995 opls_996

Re: [gmx-users] Graphene topology file

PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Graphene topology file On 7/10/14, 1:29 AM, #SUKRITI GUPTA# wrote: Hi Justin, I did simulation 2 times, once with PBC in xy with walls and other time with pbc in xyz. For pbc in xy with walls with following wall parameters: nwall = 2

Re: [gmx-users] Graphene topology file

On 7/10/14, 8:46 AM, #SUKRITI GUPTA# wrote: Hi Justin, Thanks for the reply. Following is my npt.mdp file for pbc in xy direction: title = example cpp = define = -DFLEXIBLE You shouldn't use flexible water during MD. The water models in Gromacs

Re: [gmx-users] Graphene topology file

On 7/9/14, 9:06 AM, #SUKRITI GUPTA# wrote: Thanks for the reply Justin. I just checked my box size again and found it to be smaller than the required. Hence I changed the size and ran the simulation again. This time energy minimization happened correctly without any change in the graphene

Re: [gmx-users] Graphene topology file

Subject: Re: [gmx-users] Graphene topology file On 7/9/14, 9:06 AM, #SUKRITI GUPTA# wrote: Thanks for the reply Justin. I just checked my box size again and found it to be smaller than the required. Hence I changed the size and ran the simulation again. This time energy minimization happened

Re: [gmx-users] Graphene topology file

On 7/8/14, 1:23 AM, #SUKRITI GUPTA# wrote: Hi Justin, Thanks a lot for your replies. I want to simulate a half cell with graphene electrode only on one side, hence i am using pbc in only xy direction i.e. direction of graphene sheet, so that I have a infinite size graphene sheet with no side

Re: [gmx-users] Graphene topology file

...@gromacs.org Subject: Re: [gmx-users] Graphene topology file Hi Sukriti, Can you post your .mdp file of energy minimization? The problem is not because there are no terminal H atoms. If you want periodic boundary conditions only x-y direction then you have to use nwall in .mdp file. Thanks Abhijit On Mon

Re: [gmx-users] Graphene topology file

On 7/7/14, 12:36 AM, #SUKRITI GUPTA# wrote: Hi all, After getting the topology file for graphene, when i tried to freeze graphene and do energy minimization with just water molecules around it, then the graphene structure becomes distorted ie. the upper layer of the graphene shifts down and

Re: [gmx-users] Graphene topology file

Subject: Re: [gmx-users] Graphene topology file On 7/7/14, 12:36 AM, #SUKRITI GUPTA# wrote: Hi all, After getting the topology file for graphene, when i tried to freeze graphene and do energy minimization with just water molecules around it, then the graphene structure becomes distorted ie

Re: [gmx-users] Graphene topology file

On 7/7/14, 7:54 AM, #SUKRITI GUPTA# wrote: Hi Justin, Thanks for the reply. Actually I am having the problem of z- dimension to be zero only when I am giving pbc only in xy direction. For pbc in xyz, the z dimension is not becoming zero. So do you still think it can be because of improper box

Re: [gmx-users] Graphene topology file

: Tuesday, July 8, 2014 12:44 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Graphene topology file On 7/7/14, 7:54 AM, #SUKRITI GUPTA# wrote: Hi Justin, Thanks for the reply. Actually I am having the problem of z- dimension to be zero only when I am giving pbc only in xy direction. For pbc

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

Sent: Friday, July 4, 2014 4:14 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Graphene topology file Hi Sukirti, Try the following and additionally if you want force and angle constant you can also mention in g_x2top. g_x2top -f gra.pdb -o gra.top -name GRA -nexcl 3 -pbc You have

Re: [gmx-users] Graphene topology file

Graphene topology is like for tube, so C C C ... C ... C C C C C to the N2T file and you are done. Dr. Vitaly V. Chaban On Wed, Jul 2, 2014 at 5:29 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/2/14, 9:56 AM, #SUKRITI GUPTA# wrote: Dear all, I want to simulate

Re: [gmx-users] Graphene topology file

On 7/3/14, 12:48 AM, #SUKRITI GUPTA# wrote: Dear Justin, Thanks for the reply but I am writing the .n2t file still getting the error that Could not find force field 'graphite_oplsaa' in current directory, install tree or GMXDATA path. What should I do? Moreover i don't think that n2t file

Re: [gmx-users] Graphene topology file

Hi Sukriti, Copy the oplsaa.ff directory to your working directory. Then in ffnonbonded.itp file add the following lines.. opls_995 C 612.01100 0.000 A3.4e-01 3.61200e-01 opls_996 C 612.01100 0.000 A3.4e-01 3.61200e-01 opls_997 C

Re: [gmx-users] Graphene topology file

-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of abhijit Kayal abhijitchemi...@gmail.com Sent: Thursday, July 3, 2014 6:43 PM To: gmx-us...@gromacs.org; vvcha...@gmail.com Subject: Re: [gmx-users] Graphene topology file Hi Sukriti, Copy the oplsaa.ff

[gmx-users] Graphene topology file

Dear all, I want to simulate graphite in water, for which i am trying to create a topology file for graphite. As its .rtp file cannot be written correctly, i tried to use g_x2top command following the steps given in following tutorial. http://chembytes.wikidot.com/grocnt But I think this

Re: [gmx-users] Graphene topology file

On 7/2/14, 9:56 AM, #SUKRITI GUPTA# wrote: Dear all, I want to simulate graphite in water, for which i am trying to create a topology file for graphite. As its .rtp file cannot be written correctly, i tried to use g_x2top command following the steps given in following tutorial.

Re: [gmx-users] Graphene topology file

Subject: Re: [gmx-users] Graphene topology file On 7/2/14, 9:56 AM, #SUKRITI GUPTA# wrote: Dear all, I want to simulate graphite in water, for which i am trying to create a topology file for graphite. As its .rtp file cannot be written correctly, i tried to use g_x2top command following