[gmx-users] not integer charge

 Hi all, I have not integer charge in my system (-0.11). I want to neutralize this charge by adding Na+. but I don't know how do this. I have an amino acid only in a box . adding one Na+ is wrong. because in pr step, system gives error and wrote odb file for each step. please guide me.  tnx --

Re: [gmx-users] Gromacs + Mopac error

Hi The problem is that in your first try the gaussian interface is being used, while in the second the orca interface is used. The first try should have used the mopac interface but it apparently ignored it, the reason why must be written in the configure output. Could you show the last line

Re: [gmx-users] not integer charge

On 1/8/13 3:00 AM, sara azhari wrote: Hi all, I have not integer charge in my system (-0.11). I want to neutralize this charge by adding Na+. but I don't know how do this. I have an amino acid only in a box . adding one Na+ is wrong. because in pr step, system gives error and wrote odb fi

Re: [gmx-users] selecting res CYS from G53a5 using pdb2gmx

On 1/8/13 1:37 AM, Payman Pirzadeh wrote: Dear Justin, Thanks for your suggestions. It all made sense. But I ran into a strange problem. I checked the mail list, and all I found was about misspelling the force field name. I copied the whole gromos53a5.ff directory into my working folder, copied

[gmx-users] hybrid solvent model

Hi all. I want to create a system with hybrid solvent (explicit/implicit). My system is large enough to calculate it with explicit SOL. But it is critical to study the behavior of several water molecules in the site. The idea is to generate a layer of explicit water molecules around the protein mo

Re: [gmx-users] gromacs on GPU

So could someone provide me more about gpu-accelerated MD implemented in the 4.6 gromacs ? Does it require openMM (what version is supported for that gromacs release ?) installed? By the way at present time I force with the problem of compilation 4.1.1 openMM (i need to compile openMM because of cu

[gmx-users] Re: help with improper angle in gmx

Thanks for your reply, Justin! I knew that gmx use as the follows for opls aa: ; Improper OPLS dihedrals to keep groups planar. ; (OPLS doesnt use impropers for chiral atoms). ; Since these functions are periodic of the form 1-cos(2*x), they are actually ; implemented as prope

[gmx-users] Re: help with improper angle in gmx

On 1/8/13 10:34 AM, Tom wrote: Thanks for your reply, Justin! I knew that gmx use as the follows for opls aa: ; Improper OPLS dihedrals to keep groups planar. ; (OPLS doesnt use impropers for chiral atoms). ; Since these functions are periodic of the form 1-cos(2*x), they

Re: [gmx-users] gmxcheck and GROMOS96 bonds

On 1/8/13 10:56 AM, Reid Van Lehn wrote: Hi Gromacs users, I was using gmxcheck to check a simple trajectory of surfactants, and get many errors of the type "Distance between atoms X and Y is 0.153, should be 0.023" where the actual distance is always approximately correct and the "correct" va

Re: [gmx-users] gmxcheck and GROMOS96 bonds

Will do, thank you for fast response! Reid On Tue, Jan 8, 2013 at 11:11 AM, Justin Lemkul wrote: > > > On 1/8/13 10:56 AM, Reid Van Lehn wrote: > >> Hi Gromacs users, >> >> I was using gmxcheck to check a simple trajectory of surfactants, and get >> many errors of the type "Distance between ato

[gmx-users] how to indicate solvent flexibility?

hello: I've finished a 60ns MD simulation with Gromacs and I found that the flixbility of solvent molecules inside the protein is different when it binds with different ligands: ie. in one case the solvent can move very fast with bulk environment, and in other case the solvent forms type Hb

[gmx-users] Re: help with improper angle in gmx (Justin Lemkul)

Table 5.5 does list the option of use harmonic type potential for improper dihedral. (f. tp =5) But I am confused how to build this on the ffbond.itp file and manu is not clear about this. Do you think that in the case of OPLS AA, the periodic improper dihedral is the ONLY option? Thanks a lot fo

[gmx-users] Re: help with improper angle in gmx (Justin Lemkul)

On 1/8/13 12:06 PM, Tom wrote: Table 5.5 does list the option of use harmonic type potential for improper dihedral. (f. tp =5) It's function type 2. But I am confused how to build this on the ffbond.itp file and manu is not clear about this. You would define the interaction in ffbonded.i

Re: [gmx-users] how to indicate solvent flexibility?

On 1/8/13 11:42 AM, Albert wrote: hello: I've finished a 60ns MD simulation with Gromacs and I found that the flixbility of solvent molecules inside the protein is different when it binds with different ligands: ie. in one case the solvent can move very fast with bulk environment, and in ot

Re: [gmx-users] how to indicate solvent flexibility?

My first thought was to compare the diffusion of the bulk and internal waters with g_msd. You said that in some case the internal waters forms hydrogen bonds with the protein. I think that in this case a plot showing this would be nice too. 2013/1/8 Justin Lemkul > > > On 1/8/13 11:4

Re: [gmx-users] hybrid solvent model

I'm also interested in doing this with GROMACS but couldn't find a way yet. In my case I'm interested in applying it to REMD simulations in which large conformational changes occur, which makes the implementation more difficult because the shape of the water layer would be irregular and change

RE: [gmx-users] selecting res CYS from G53a5 using pdb2gmx

Dear Justin, Thanks for the tips. Things worked smoothly up to the point when I wanted to run an actual simulation. When I wanted to run grompp for a NVT simulation, I got this error message: Fatal error: 7 atoms are not part of any of the T-Coupling groups I realized that that in my mdp file, I

Re: [gmx-users] selecting res CYS from G53a5 using pdb2gmx

On 1/8/13 6:09 PM, Payman Pirzadeh wrote: Dear Justin, Thanks for the tips. Things worked smoothly up to the point when I wanted to run an actual simulation. When I wanted to run grompp for a NVT simulation, I got this error message: Fatal error: 7 atoms are not part of any of the T-Coupling g

RE: [gmx-users] selecting res CYS from G53a5 using pdb2gmx

These are the lines in my residuetype.dat: CYS Protein CYS1Protein CYS2Protein CYSHProtein CYA Protein DALAProtein Have I missed anything? How can I couple CYA with protein under this conditions? Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailt

RE: [gmx-users] selecting res CYS from G53a5 using pdb2gmx

Hi, Found my solution; made an index file which had the protein and CYA in the same group. Thanks for all your helps Justin. P. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin Lemkul Sent: January-08-13 4:13 PM To: Discussi

Re: [gmx-users] selecting res CYS from G53a5 using pdb2gmx

On 1/8/13 6:58 PM, Payman Pirzadeh wrote: Hi, Found my solution; made an index file which had the protein and CYA in the same group. Thanks for all your helps Justin. I'm glad you found a solution, but for the purpose of being thorough I need to say that this should not be necessary. A res

RE: [gmx-users] selecting res CYS from G53a5 using pdb2gmx

I had modified three files: aminoacids.rtp, aminoacids.hdb and residuetypes.dat. All these modifications were done prior running pdb2gmx. So, I will be glad if you could let me know what the problem is. Best, Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-

Re: [gmx-users] selecting res CYS from G53a5 using pdb2gmx

On 1/8/13 7:25 PM, Payman Pirzadeh wrote: I had modified three files: aminoacids.rtp, aminoacids.hdb and residuetypes.dat. All these modifications were done prior running pdb2gmx. So, I will be glad if you could let me know what the problem is. From that description, everything should be fine

RE: [gmx-users] selecting res CYS from G53a5 using pdb2gmx

Since gromacs is globally installed on the cluster, I am making local modifications. What was strange was I modified the three files, and I ran pdb2gmx with them, and it failed (it could not find certain atoms?!). Then I copied the whole gromos53a5 folder to my working directory and moved these fil

Re: [gmx-users] selecting res CYS from G53a5 using pdb2gmx

On 1/8/13 8:05 PM, Payman Pirzadeh wrote: Since gromacs is globally installed on the cluster, I am making local modifications. What was strange was I modified the three files, and I ran pdb2gmx with them, and it failed (it could not find certain atoms?!). Then I copied the whole gromos53a5 fold

RE: [gmx-users] selecting res CYS from G53a5 using pdb2gmx

Dear Justin, You are absolutely right. I only needed to keep the modified 'residuetypes.dat' in my working directory not the .rtp and .hdb files. I retried the whole process and this time CYA was not a separate group. Great experience. Thanks for your patience and help. Best, Payman -Origina

Re: [gmx-users] gromacs on GPU

On Tue, Jan 8, 2013 at 3:22 PM, James Starlight wrote: > So could someone provide me more about gpu-accelerated MD implemented > in the 4.6 gromacs ? Does it require openMM (what version is supported > FYI, if nobody can, trust G: http://lmgtfy.com/?q=gromacs+4.6+gpu+acceleration http://lmgtfy.co

Re: [gmx-users] enough time for simulation

Dear Mohammad, I am not a specialist in gromacs. To observe these phenomenon the time scale is much up to 1microsecond . So which forcefield you decided to use ??? People generally use Martini Coarse Grain FF for these type of work. You have to run the system up to you reach your desire result.

[gmx-users] force field for GPI ligands which has lipid and carbohydrates ?

Could you tell me which force field recognizes the GPI ligand which posses lipid and mannose which interacts with protein? -- 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_