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 to mention periodic_molecules=yes in the .mdp file. Thanks Abhijit On Fri, Jul 4, 2014 at 1:04 PM, #SUKRITI

Re: [gmx-users] why the energy items in gromacs is different from charmm?

On Fri, Jul 4, 2014 at 6:44 AM, wliu w...@itcs.ecnu.edu.cn wrote: Hi, I have a following issue: I use the force field CHARMM22-CMAP (that is charmm27-CMAP) in gromacs to calculate the chignolin.pdb, I want to know the energy items of just this one conformation. I choose to run a very

Re: [gmx-users] help with poor performance on gromacs on Cray linux

On Sat, Jun 28, 2014 at 11:44 PM, Tom dna...@gmail.com wrote: Dear Mark, Thanks a lot for your kind help! I notice this on the head of *log file. It is saying *Binary not matching hardware - you might be losing performance.Acceleration most likely to fit this hardware:

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,

[gmx-users] Minimisation failure: The charge group moved more than the distance allowed by the domain decomposition

Here all my files: https://www.dropbox.com/s/94u9b9stsk84ckz/1oyn6wat1994-15a_vconf-docking_1.tar.bz2 I try minimize this with: grompp_mpi_d -maxwarn 2 -f ~/emamber.mdp -c *_solvated_bonded_GMX.gro -p *_solvated_bonded_GMX.top -o em.tpr mdrun_mpi_d -deffnm em Here is my emamber.mdp file:

[gmx-users] [ pairs_nb ] in topology

Dear all, Does anyone know how to write [ pairs_nb ] in topology? I read the Manual 4.6.5, only chapter 5.3.4 and Table 5.5 described the [ pairs_nb ]. Based on Table 5.5, I wrote like this: [ pairs_nb ] 1 2 1 -0.044600 -0.162400 3.39967e-01 3.59824e-01 But I got an error like this: case: 20

Re: [gmx-users] confout.gro

The error message says that the perl script could not find a file named confout.gro. Either generate one or put it in the correct directory, so the script can find it. Victor 2014-07-04 3:48 GMT-05:00 RINU KHATTRI nickname.mi...@gmail.com: hello gromacs users now i am at minimization step

[gmx-users] question about Computational Electrophysiology

Dear GMX developers, The functionality of version of 5.0 about Computational Electrophysiology looks nice. Ions concentration can be maintaied to a fixed value. There are options for controlling ion concentration in each compartment. I am wondering if water (or solvent) concentration can be

[gmx-users] simulation at acid medium

Dear all Please, I need help. I have to do a simulation at an acid medium (PH = around 5 or 6). Is it sufficient to work with normal water,from it to create a physiological solution (Ph=around 5) and then to work with the physiological solution? I would very much appreciate any clues in this

Re: [gmx-users] simulation at acid medium

Hi Chris, This very much depends on what system you are studying and what properties you aim to look at. Could you provide more detail please. Kind regards, Erik Erik Marklund, PhD Postdoctoral Research Associate Department of Chemistry Physical Theoretical Chemistry Laboratory University of

Re: [gmx-users] simulation at acid medium

Hi Erik Thanks. Details: System: proteins Properties: those ones for which there are analyzes tools in Gromacs I am trying to model some proteins at acid medium. I use MD with water and I create a physiological solution from the counterion tool of Gromacs, But I think something is wrong.

Re: [gmx-users] simulation at acid medium

Then you essentially need to protonate the side chains according to their pKa and the pH. Note that the protons will not hop around between groups in normal MD. What makes you think something's wrong with your physiological solution? Kind regards, Erik On 4 Jul 2014, at 19:47,