gmx-users@gromacs.org

of the paper that are were related to amber but I could not find the partial charge of atoms in amber force field and for decane, How can I find the partial charge of atoms in decane? -- Sincerely Ali Alizadeh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman

gmx-users@gromacs.org

Dear All users I want to use amber ff and there are some particles in my system that non bonded interaction between them is buckingham, Can I simulate this system in gromacs with different cut-off? -- Sincerely Ali Alizadeh -- gmx-users mailing listgmx-users@gromacs.org http

[gmx-users] Re: gmx-users Digest, Vol 106, Issue 101

Dear Justin Thank you for your reply, > > > On 2/19/13 4:57 PM, Ali Alizadeh wrote: >> Dear All users >> >> There are a wall(a gold crystal with 111 orientation) and a bulk of >> fluid(alkane) in my simulation box, >> >> My problem is, Is it poss

[gmx-users] Questions about parameters in topology file

Dear Justin Thank you very much for your reply, On 2/9/13 3:14 AM, Ali Alizadeh wrote: > Dear All user > > I am using oplsa.ff( in forcefield.itp : oplsa use combination rule 3 > , A part of my topology file, > > Can I use my parameters instead of force filed parameters in

[gmx-users] Re: gmx-users Digest, Vol 102, Issue 117

Dear Justin Thank you for your reply, Sincerely -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to

[gmx-users] Re: gmx-users Digest, Vol 102, Issue 112

Dear Justin Please check my commands, Are these correct, step by step? If these are correct then i will start my simulation with longer time, 1- pdb2gmx -f mixture.pdb -o mix -p mix 2- editconf -f mix.gro -o mix2.pdb ; for obtain a clean .pdb for obtaining clean .gro and clean .top 3- pdb2

[gmx-users] Re: gmx-users Digest, Vol 102, Issue 99

Dear Justin Thank you for your reply, On 10/16/12 7:55 AM, Ali Alizadeh wrote: > Dear All users > > 1- When i use these commands for generating number density profile > > I see completely different results(in z direction, length in z > direction is 8, number density versus o

[gmx-users] Re: gmx-users Digest, Vol 102, Issue 52

Dear usres Thank you for your replies 1- Is it possible define a ion as a propane molecule and then I do adding propane molecules instead of methane molecules in my system? 2- Other wise, I select 300 molecules of methane and remove them from my system(randomly and by hand, for example 500 mole

[gmx-users] Fwd: How to can i replace a molecule

Dear All users How to can i replace a molecule(for example methane) with another molecule(propane)? Number of these molecules are given and their position is random, Can I use genbox or genion, How to do i do it? Sincerely -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.

[gmx-users] Re: gmx-users Digest, Vol 101, Issue 68

Dear Justin For example, In that tutorial(box vector : 3 , 3 , 10), At first, I add cyclo hexane into my system( center: 3 ,3 ,1) Then I add water with certain certain thickness(center: 3 , 3 , 5) Then I want to add cyclo hexane into my system( center: 3 ,3 , 8) Is it possible? How to? Sincerel

[gmx-users] How to a .gro file generated from this .top file?

Dear Justin I prepare a .top file with a combination of input #include and pdb2gmx, How can i generate a .gro file from this .top file? Sincerely -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gro

[gmx-users] Re: gmx-users Digest, Vol 101, Issue 56

Dear Justin Thank you so much, Sincerely -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the li

[gmx-users] Re: gmx-users Digest, Vol 101, Issue 17

Dears Justin and Christopher Thanks a lot, I'll do the same. Sincerely -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (

[gmx-users] How to add new residue(LIG reisdue)?

Dear all users In my pdb file that contain ethane or propane or other molecules, there are LIG residue in my pdb file that gromacs could not found them, how to add this LIG(in our pdb files) for my force field? This residue(LIG) exists in all pdb files for each simple molecules, Sincerely -- gm

[gmx-users] FATAL ERROR Residue "LIG" not found in residue topology database?

Dear All usres: I am trying to do a simple system that contains 4 molecules ethane and MD run using GROMACS. I build my .pdb file by using Avogadro software . Afterwards, I try to generate the topology and .gro file using pdb2gmx program and it generates an error. I am using the 43a1 force field.

[gmx-users] FATAL ERROR: Residue "LIG" not found in residue topology database.

Dear All usres: I am trying to do a simple system that contains 4 molecules ethane and MD run using GROMACS. I build my .pdb file by using Avogadro software . Afterwards, I try to generate the topology and .gro file using pdb2gmx program and it generates an error. I am using the 43a1 force field.

[gmx-users] How to generated a .gro file for a special molecules?

Dear All users: How to generated a .gro file for a special molecules? For example: Tutorial 4: Biphasic Systems http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/biphasic/index.html sincerely, -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailm

[gmx-users] What is The gromacs tutorial output files?

Dear all user, I'm a gromacs beginner and have a quick question. I installed gromacs 4.5.5 online on ubuntu12.04. How do I check that it is correctly installed? and, What is The gromacs tutorial output files? I could not get them tpr file. Please help me. -- gmx-users mailing listgmx-u