[gmx-users] convergence of MD simulations,

structure, interface between fluid and solid) after 1ns simulation my temperature fluctuation shows quite convergence, my total energy corroborates this convergence too. -- Sincerely Ali Alizadeh -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support

Re: [gmx-users] convergence of MD simulations,

Dear Justin, Thank you very much for your reply and especially your time. According to my structural analysis my convergence sounds good as you mentioned, my diffusion coefficients, RDF, number density profiles over different time intervals show stable states. Ali Alizadeh Justin wrote: Neither

[gmx-users] Eror: No parallel Ewald use PME instead!

suggestions? -- Sincerely Ali Alizadeh -- 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

Re: [gmx-users] Eror: No parallel Ewald use PME instead!

. What's your point on it? - Mark wrote: Hi, What makes you think the PME algorithm, rather than your choices of settings for it (and twenty other things), is the problem? Mark On Wed, Jun 4, 2014 at 7:57 AM, Ali Alizadeh ali.alizadehmojarad at gmail.com https://maillist.sys.kth.se

Re: [gmx-users] Eror: No parallel Ewald use PME instead!

I performed an NVT simulation. On Wed, Jun 4, 2014 at 3:12 PM, Ali Alizadeh ali.alizadehmoja...@gmail.com wrote: Dear Mark, Thank you for your reply. When you do not change any parameters except one thing in mdp file(PME to ewald as the paper said that)and then your system converges

Re: [gmx-users] Eror: No parallel Ewald use PME instead!

= no ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr = EnerPres ; Velocity generation gen_vel = yes gen_temp = 300 gen_seed = -1 On 6/4/14, 8:29 AM, Ali Alizadeh wrote: Dear Mark, In my first simulation we had these lines: ; Electrostatics coulombtype

Re: [gmx-users] NPT simulation stage

is enough for the NPT stage? Regards On Monday, April 28, 2014 12:48 PM, Ali Alizadeh ali.alizadehmoja...@gmail.com wrote: Dear Mahboobeh, I do not know what component your system includes. However, based on my experiences, the fluctuation of pressure is high especially for small

[gmx-users] Non-neutral system

neutralization can be done by uniform neutralizing background charge. Which part of gromacs do it? -- Sincerely Ali Alizadeh -- 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

Re: [gmx-users] Non-neutral system

. However, if the charges in your system are distributed inhomogeneously (as, e.g. in a water/membrane system), you will get artefacts, as described in http://www.mpibpc.mpg.de/14063977/Hub_2014_JCTC.pdf Best, Carsten On 23 Apr 2014, at 12:58, Ali Alizadeh ali.alizadehmojarad at gmail.com https

Re: [gmx-users] Problem with radius of gyration calculation

VMD is an alternative, it was my suggestion. I know my similar was similar to ignoring the original questions. Besides, he can calculate end to end distance if he wants. Anyway, you are right:). On Thu, Feb 6, 2014 at 4:32 AM, Ali Alizadeh ali.alizadehmoja...@gmail.comwrote: Dear Jernej

Re: [gmx-users] Density profile for COM of residues

? Besides, In VMD I have written a tcl code for doing it but I can extract every COM in every frame. So I do not know how I can implement time averaging. Hamid wrote: Dlpoy or gromacs? On Mon, Dec 30, 2013 at 3:49 PM, Ali Alizadeh ali.alizadehmoja...@gmail.com wrote: Dear All users, I

[gmx-users] Density profile for COM of residues

Dear All users, I want to calculate the number density profile for COM of my residues. They are located on a surface. Are there any options for counting COMs respect to that surface? -- Sincerely Ali Alizadeh -- Gromacs Users mailing list * Please search the archive at http

[gmx-users] Density profile for COM of residues,

Dear All users, I want to calculate the number density profile for COM of my residues. They are located on a surface. Are there any options for counting COMs respect to that surface? -- Sincerely Ali Alizadeh -- Gromacs Users mailing list * Please search the archive at http

Re: [gmx-users] Potential energy

Dear Justin, Thank you very much for your reply. One point, why useless??? You meant this potential calculation is useless? On Sat, Dec 28, 2013 at 2:30 AM, Ali Alizadeh ali.alizadehmoja...@gmail.com wrote: Dear All users, I have a question about calculation of potential energy