[gmx-users] g_energy for comparing total energies of 2 similar systems

g%3D=h9cz1GMp80awqK7uWU0tmwAfbhpQFtMYCkfwOWcjFqjCjKA5rnYYMRF4FV7Oec3YWfk_SWGzz4s.] Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI@N) | Nanyang Technological University N1.3-B4-14, 50 Nanyang Avenue, Singapore 639798 Tel: (65) 81164191 GMT+8h | Email:sukriti...@e.ntu.edu.sg | Web:erian.ntu.edu.sg<http://www.ntu

Re: [gmx-users] rlist, rcolumb, and rvdw

achment?id=AAMkADNjYmY4NDc0LTVjMzUtNDNmOC1hYzdkLTU5NTZhODkwYjVhNwBGAACBUPJnHBz9Qb1jEGoiHu01BwCW%2B40K8EMKR52f2bViS6X0NaBFAAC1PvQTaUN0S5CzEDGS8lwUAAIr8o3VAAABEgAQAIhFug57qj9Lg6WQKih11Lg%3D=h9cz1GMp80awqK7uWU0tmwAfbhpQFtMYCkfwOWcjFqjCjKA5rnYYMRF4FV7Oec3YWfk_SWGzz4s.=3] Sukriti Gupta (Ms) | PhD Student | Energy Research

[gmx-users] Group vs Verlet cutoff scheme

=h9cz1GMp80awqK7uWU0tmwAfbhpQFtMYCkfwOWcjFqjCjKA5rnYYMRF4FV7Oec3YWfk_SWGzz4s.=3] Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI@N) | Nanyang Technological University N1.3-B4-14, 50 Nanyang Avenue, Singapore 639798 Tel: (65) 81164191 GMT+8h | Email:sukriti...@e.ntu.edu.sg | Web:erian.ntu.edu.sg<h

Re: [gmx-users] Charged systems

%2B40K8EMKR52f2bViS6X0NaBFAAC1PvQTaUN0S5CzEDGS8lwUAAIr8o3VAAABEgAQAIhFug57qj9Lg6WQKih11Lg%3D=h9cz1GMp80awqK7uWU0tmwAfbhpQFtMYCkfwOWcjFqjCjKA5rnYYMRF4FV7Oec3YWfk_SWGzz4s.=3] Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI@N) | Nanyang Technological University N1.3-B4-14, 50 Nanyang Avenue, Singapore 639798 Tel: (65) 81164191 GMT+8h | Email:sukriti

Re: [gmx-users] Problem in running energy minimization in Gromacs 5.1.2 version

%2B40K8EMKR52f2bViS6X0NaBFAAC1PvQTaUN0S5CzEDGS8lwUAAIr8o3VAAABEgAQAIhFug57qj9Lg6WQKih11Lg%3D=h9cz1GMp80awqK7uWU0tmwAfbhpQFtMYCkfwOWcjFqjCjKA5rnYYMRF4FV7Oec3YWfk_SWGzz4s.=3] Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI@N) | Nanyang Technological University N1.3-B4-14, 50 Nanyang Avenue

Re: [gmx-users] Problem in running energy minimization in Gromacs 5.1.2 version

=AAMkADNjYmY4NDc0LTVjMzUtNDNmOC1hYzdkLTU5NTZhODkwYjVhNwBGAACBUPJnHBz9Qb1jEGoiHu01BwCW%2B40K8EMKR52f2bViS6X0NaBFAAC1PvQTaUN0S5CzEDGS8lwUAAIr8o3VAAABEgAQAIhFug57qj9Lg6WQKih11Lg%3D=h9cz1GMp80awqK7uWU0tmwAfbhpQFtMYCkfwOWcjFqjCjKA5rnYYMRF4FV7Oec3YWfk_SWGzz4s.=3] Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI@N) | Nanyang Technological University N1.3

Re: [gmx-users] Problem in running energy minimization in Gromacs 5.1.2 version

%2B40K8EMKR52f2bViS6X0NaBFAAC1PvQTaUN0S5CzEDGS8lwUAAIr8o3VAAABEgAQAIhFug57qj9Lg6WQKih11Lg%3D=h9cz1GMp80awqK7uWU0tmwAfbhpQFtMYCkfwOWcjFqjCjKA5rnYYMRF4FV7Oec3YWfk_SWGzz4s.=3] Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI@N) | Nanyang Technological University N1.3-B4-14, 50 Nanyang Avenue, Singapore 639798 Tel: (65) 81164191 GMT+8h | Email:sukriti

[gmx-users] Problem in running energy minimization in Gromacs 5.1.2 version

01BwCW%2B40K8EMKR52f2bViS6X0NaBFAAC1PvQTaUN0S5CzEDGS8lwUAAIr8o3VAAABEgAQAIhFug57qj9Lg6WQKih11Lg%3D=h9cz1GMp80awqK7uWU0tmwAfbhpQFtMYCkfwOWcjFqjCjKA5rnYYMRF4FV7Oec3YWfk_SWGzz4s.=3] Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI@N) | Nanyang Technological University N1.3-B4-14, 50 Nanyang Avenue, Singapore 639798 Tel: (65) 81164191 GMT+8h | Email:s

[gmx-users] Charged systems

%2B40K8EMKR52f2bViS6X0NaBFAAC1PvQTaUN0S5CzEDGS8lwUAAIr8o3VAAABEgAQAIhFug57qj9Lg6WQKih11Lg%3D=h9cz1GMp80awqK7uWU0tmwAfbhpQFtMYCkfwOWcjFqjCjKA5rnYYMRF4FV7Oec3YWfk_SWGzz4s.=3] Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI@N) | Nanyang Technological University N1.3-B4-14, 50 Nanyang Avenue, Singapore 639798 Tel: (65) 81164191 GMT+8h | Email:sukriti

Re: [gmx-users] Energy group exclusions

%3D=h9cz1GMp80awqK7uWU0tmwAfbhpQFtMYCkfwOWcjFqjCjKA5rnYYMRF4FV7Oec3YWfk_SWGzz4s.=3] Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI@N) | Nanyang Technological University N1.3-B4-14, 50 Nanyang Avenue, Singapore 639798 Tel: (65) 81164191 GMT+8h | Email:sukriti

[gmx-users] Energy group exclusions

as my system has only only frozen molecule so there won't be any atom - atom non bonded interaction anyways between 2 frozen atoms, however within this molecule I have 3 atoms, so will their non bonded interaction also cause unrealistic energy values? Thanks Sukriti Gupta -- Gromacs Users

[gmx-users] energy_group exclusions

exclusions as my system has only only frozen molecule so there won't be any atom - atom non bonded interaction anyways between 2 frozen atoms, however within this molecule I have 3 atoms, so will their non bonded interaction also cause unrealistic energy values? Thanks Sukriti Gupta [https

[gmx-users] Query regarding the use of g_energy command to extract free energies

=AAMkADNjYmY4NDc0LTVjMzUtNDNmOC1hYzdkLTU5NTZhODkwYjVhNwBGAACBUPJnHBz9Qb1jEGoiHu01BwCW%2B40K8EMKR52f2bViS6X0NaBFAAC1PvQTaUN0S5CzEDGS8lwUAAIr8o3VAAABEgAQAIhFug57qj9Lg6WQKih11Lg%3D=h9cz1GMp80awqK7uWU0tmwAfbhpQFtMYCkfwOWcjFqjCjKA5rnYYMRF4FV7Oec3YWfk_SWGzz4s.=3] Sukriti Gupta (Ms) | PhD Student | Energy Research

Re: [gmx-users] Sulfate ion parameters

Dear Mark, Thanks for the reply. Actually, I emailed the corresponding author but didn't get any reply. Also, it is not mentioned in the paper that the model is for a rigid system. Regards Sukriti Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI@N) | Nanyang

Re: [gmx-users] Sulfate ion parameters

nd bending and stretching parameters. Is there a way to find what parameters were used in the study. Thanks and Regards Sukriti Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI@N) | Nanyang Technological University N1.3-B4-14, 50 Nanyang Avenue, Singapore 639798 Tel: (65) 81164

[gmx-users] Sulfate ion parameters

=h9cz1GMp80awqK7uWU0tmwAfbhpQFtMYCkfwOWcjFqjCjKA5rnYYMRF4FV7Oec3YWfk_SWGzz4s.=3] Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI@N) | Nanyang Technological University N1.3-B4-14, 50 Nanyang Avenue, Singapore 639798 Tel: (65) 81164191 GMT+8h | Email:sukriti...@e.ntu.edu.sg | Web:erian.ntu.edu.sg<http://www.ntu.edu.sg/h

[gmx-users] adding polyatomic species in water

dumped). I also tried using genconf but still i was getting the same problem. Can anyone please let me know what is wrong with my system and how can i correctly add all the species in my system. Regards Sukriti [https://wis.ntu.edu.sg/graphics/tms/ntulogofit2.gif] Sukriti Gupta (Ms) | PhD

[gmx-users] Adding metal ions near graphene sheet

://wis.ntu.edu.sg/graphics/tms/ntulogofit2.gif] Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI@N) | Nanyang Technological University N1.3-B4-14, 50 Nanyang Avenue, Singapore 639798 Tel: (65) 81164191 GMT+8h | Email:sukriti...@e.ntu.edu.sg | Web:erian.ntu.edu.sghttp://www.ntu.edu.sg/home

[gmx-users] Lennard jones and bonded opls aa parameters for sulfate ions

] Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI@N) | Nanyang Technological University N1.3-B4-14, 50 Nanyang Avenue, Singapore 639798 Tel: (65) 81164191 GMT+8h | Email:sukriti...@e.ntu.edu.sg | Web:erian.ntu.edu.sghttp://www.ntu.edu.sg/home/xuzc/People.html -- Gromacs

Re: [gmx-users] Graphene topology file

and Regards Sukriti Gupta Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI@N) | Nanyang Technological University N1.3-B4-14, 50 Nanyang Avenue, Singapore 639798 Tel: (65) 81164191 GMT+8h | Email:sukriti...@e.ntu.edu.sg | Web:erian.ntu.edu.sg

[gmx-users] Lennard jones parameters for metal ions

it will be same because vander waals radii is defined for a element and not ion, hence it will be same for Fe or Fe+2 or Fe+3. Regards Sukriti [https://wis.ntu.edu.sg/graphics/tms/ntulogofit2.gif] Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI@N) | Nanyang

[gmx-users] Lennard jones parameters for ions

it will be same because vander waals radii is defined for a element and not ion, hence it will be same for Fe or Fe+2 or Fe+3. Regards Sukriti [https://wis.ntu.edu.sg/graphics/tms/ntulogofit2.gif] Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI@N) | Nanyang Technological

Re: [gmx-users] Lennard jones parameters for ions

-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Justin Lemkul jalem...@vt.edu Sent: Friday, July 25, 2014 7:46 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Lennard jones parameters for ions On 7/25/14, 7:39 AM, #SUKRITI GUPTA# wrote: Dear

Re: [gmx-users] Graphene topology file

a layer of vacuum, wont the box size reduce in npt and cause this error? Should I skip npt and directly do nvt? Regards Sukriti Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI@N) | Nanyang Technological University N1.3-B4-14, 50 Nanyang Avenue, Singapore 639798 Tel: (65

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) | PhD Student | Energy Research Institute @ NTU (ERI@N) | Nanyang Technological

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

mail the images to your mail id? Regards Sukriti Gupta Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI@N) | Nanyang Technological University Interdisciplinary Graduate School | Office: N1.3-B4-14, 62 Nanyang Drive, Singapore(637459) Tel: (65

Re: [gmx-users] Graphene topology file

and Regards Sukriti Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI@N) | Nanyang Technological University Interdisciplinary Graduate School | Office: N1.3-B4-14, 62 Nanyang Drive, Singapore(637459) Tel: (65) 81164191 GMT+8h | Email:sukriti

Re: [gmx-users] Graphene topology file

freezedim = Y Y Y Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI@N) | Nanyang Technological University Interdisciplinary Graduate School | Office: N1.3-B4-14, 62 Nanyang Drive, Singapore(637459) Tel: (65) 81164191 GMT+8h | Email:sukriti

Re: [gmx-users] Graphene topology file

and Regards Sukriti Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI@N) | Nanyang Technological University Interdisciplinary Graduate School | Office: N1.3-B4-14, 62 Nanyang Drive, Singapore(637459) Tel: (65) 81164191 GMT+8h

Re: [gmx-users] Graphene topology file

carbons. I don't know what is the problem with my system. Regards Sukriti Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI@N) | Nanyang Technological University Interdisciplinary Graduate School | Office: N1.3-B4-14, 62 Nanyang Drive

Re: [gmx-users] Graphene topology file

Hi Abhijit, Thanks for the reply. Now it is working. Regards Sukriti Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI@N) | Nanyang Technological University Interdisciplinary Graduate School | Office: N1.3-B4-14, 62 Nanyang Drive

Re: [gmx-users] Graphene topology file

Dear Justin and Abhijit, Thanks a lot for your help. Now I am able to make the topology file but while doing grompp for energy minimisation its not taking the dihedral values on its own. Regards Sukriti Sukriti Gupta (Ms) | PhD Student | Energy Research

[gmx-users] Graphene topology file

=27 Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI@N) | Nanyang Technological University http://maps.ntu.edu.sg/maps#q:research%20techno%20plaza%20%28rtp%29 Interdisciplinary Graduate School | Office: N1.3-B4-14, 62 Nanyang Drive, Singapore(637459) Tel: (65) 81164191 GMT+8h

Re: [gmx-users] Graphene topology file

. Regards Sukriti Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI@N) | Nanyang Technological University Interdisciplinary Graduate School | Office: N1.3-B4-14, 62 Nanyang Drive, Singapore(637459) Tel: (65) 81164191 GMT+8h | Email:sukriti