Re: [gmx-users] partial atomic charges

On 4/10/2011 5:20 PM, MARY VARUGHESE wrote: Hi, I , am working on interaction between proteins/nucleic acids and ligands. On deriving partial atomic charges using gaussian can anyone suggest, among HF-6-31G* and B3LYP-6-31G which one is ideal(or any other one to suggest) and why? I mean to get

[gmx-users] partial atomic charges

Hi, I , am working on interaction between proteins/nucleic acids and ligands. On deriving partial atomic charges using gaussian can anyone suggest, among HF-6-31G* and B3LYP-6-31G which one is ideal(or any other one to suggest) and why? I mean to get the partial atomic charges of the ligand

Re: [gmx-users] MD with membrane protein

On Tue, Oct 4, 2011 at 2:57 AM, elisa carli wrote: > Hi Lisa > Thank you very much for your reply. > After minimimization could I run a molecular dynamic production? > Or have I to do other sets? > Yes, after energy minimization, you need do some other sets (like NVT and NPT). Could you write me

RE: [gmx-users] Free Energy Question

I think using Perturbation method is more appropriate for this kind of free energy calculation. Check Leach, Molecular Modelling Principle and Applications pp 554-568. Its clearly described there and you can implement it in GROMACS. Cheers, Emanuel

Re: [gmx-users] heteroatom not to be a ligand

ahmet yıldırım wrote: Dear users, I have a xxx .pdb including enzyme+X. But X is a cryoprotectant, that is heteroatom, it is not a ligand. I think I shouldn't use a way as Justin tutorial 5. Because X is not a ligand. what should I do? If it's not relevant to the dynamics (as is often th

[gmx-users] heteroatom not to be a ligand

Dear users, I have a xxx .pdb including enzyme+X. But X is a cryoprotectant, that is heteroatom, it is not a ligand. I think I shouldn't use a way as Justin tutorial 5. Because X is not a ligand. what should I do? Thanks -- Ahmet YILDIRIM -- gmx-users mailing listgmx-users@gromacs.org http

Re: [gmx-users] RMSD bonds and angles

I look at chapter 8 but I didnt found that I want. can you give a hint? Thanks 2011/10/3 Mark Abraham > On 3/10/2011 10:29 PM, ahmet yıldırım wrote: > >> Dear users, >> >> How can I calculate the RMSD bonds (A˚ ) and RMSD angles (o)? >> > > Please start your search in chapter 8 of the manual, an

[gmx-users] Free Energy Question

Hello all, I have a general question about calculating free energies. I recently used g_bar to calculate the free energies of decoupling coulombic and vdW forces of a solute molecule in solvent. I now need to calculate the free energy of a solute molecule mutating to a new molecule (identical bu

Re: [gmx-users] MD with membrane protein

elisa carli wrote: Hi Lisa Thank you very much for your reply. After minimimization could I run a molecular dynamic production? Or have I to do other sets? Could you write me which are the commands to execute up to MD run? http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_S

Re: [gmx-users] MD with membrane protein

Hi Lisa Thank you very much for your reply. After minimimization could I run a molecular dynamic production? Or have I to do other sets? Could you write me which are the commands to execute up to MD run? Bests 2011/9/22 lina > On Thu, Sep 22, 2011 at 11:34 AM, elisa carli wrote: > >> Dear All

Re: [gmx-users] pull code problem: between protofilaments

Dear Chris, Thank a lot for your reply. I am trying the pull code that you have suggested. And I would be more specific about the problem and code in my future mails. regards, Shilpi On 02/10/11, chris.ne...@utoronto.ca wrote: > Dear Shilpi: > > Can you use something like this? > > pull 

Re: [gmx-users] make_ndx and rdf

oguz gurbulak wrote: Dear Justin, Of course I tried typing "help" at the make_ndx prompt but I couldn't generate a .ndx file for my purposes. I strongly need expert help for OK, you didn't say that. You said you tried the mailing list, manual, and the wiki was unavailable. The "help"

Re: [gmx-users] make_ndx and rdf

Dear Justin, Of course I tried  typing "help" at the make_ndx prompt but I couldn't generate a .ndx file for my purposes.  I strongly need expert help for using make_ndx tool. I'm trying to generate .ndx file for more than one week. Finally I decided to ask it to mailing list. So I will be appr

[gmx-users] About the GROMOS96 parameters files

Shame on me!! Indeed, you are right Justin. I have misread the paper. I don't know why I cited GROMOS96. Sorry all for wasting your time with these silly questions. Stephane -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search

Re: [gmx-users] make_ndx and rdf

Molecular Dynamics wrote: Dear All, I want to calculate rdf for carbon-oxygen, carbon-hydrogen and carbon-water using g_rdf but how can I generate an .ndx file that are suitable for these systems ? I searched mailing list and read manual but couldn't generate .ndx file using make_ndx tool.

[gmx-users] make_ndx and rdf

Dear All, I want to calculate rdf for carbon-oxygen, carbon-hydrogen and carbon-water using g_rdf but how can I generate an .ndx file that are suitable for these systems ? I searched mailing list and read manual but couldn't generate .ndx file using make_ndx tool. However, I tried to see the ma

[gmx-users] RE:How to change the screen's output frequency?

Speaking of which, I think that all programs should by default list -hidden when they are run with -h so that users are aware that there are hidden options and know how to access them. The -h output could clearly indicate that such options are not fully tested, etc. Chris. Justin A. Lemkul

Re: [gmx-users] RE:How to change the screen's output frequency?

杜波 wrote: On 2011-10-02 17:14, 杜波 wrote: How to change the screen's output frequency? ol 0.85 imb F 6% step 4188000, remaining runtime: 174 s vol 0.87 imb F 3% step 4188100, remaining runtime: 174 s vol 0.86 imb F 1% step 4188200, remaining runtime: 174 s vol 0.86 imb F 4% s

[gmx-users] RE:How to change the screen's output frequency?

On 2011-10-02 17:14, 杜波 wrote: > How to change the screen's output frequency? > > ol 0.85 imb F 6% step 4188000, remaining runtime: 174 s > vol 0.87 imb F 3% step 4188100, remaining runtime: 174 s > vol 0.86 imb F 1% step 4188200, remaining runtime: 174 s > vol 0.86 imb F 4% step

Re: [gmx-users] Regarding 1-d free energy profile from g_sham

bipin singh wrote: Thanks for your reply. I have attached two figures here. The first figure 1d_fel is, what I am trying to get through g_sham and the second figure 1d_fel_sham is what I got from g_sham. The bindex.ndx file contains the frame indices for each bins.Now the problem is how to

Re: [gmx-users] Regarding 1-d free energy profile from g_sham

bipin singh wrote: Hello, I am using g_sham to plot a one dimensional free energy profile for a given reaction coordinate( in my case it is first principal component(PC1) from a principal component analysis). It gives me the bin index Vs free energy plot, but I want PC's value Vs free energ

Re: [gmx-users] About the GROMOS96 parameters files

intra\sa175950 wrote: Dear GMXusers, I would like to reproduce the results obtained in the paper of Marrink et al "Molecular dynamics simulations of the kinetics of spontaneous micelle formation". J. Phys. Chem. B, 104:12165-12173, 2000". In this (old but interesting) work, the authors used

Re: [gmx-users] RMSD bonds and angles

On 3/10/2011 10:29 PM, ahmet yıldırım wrote: Dear users, How can I calculate the RMSD bonds (A˚ ) and RMSD angles (o)? Please start your search in chapter 8 of the manual, and consider doing some tutorial material. Someone is likely to have covered some similar procedures. Mark -- gmx-user

Re: [gmx-users] analyzing protein conformation stability

On 03/10/11, *Sajad Ahrari * wrote: Hello Dear users is there any command in gromacs for analysis of protein stability? or I should be using those related to calculation of B-factor? That's an extremely complex thing to attempt to measure. The observables in MD simulations are the posit

[gmx-users] RMSD bonds and angles

Dear users, How can I calculate the RMSD bonds (A˚ ) and RMSD angles (o)? Thanks in advance -- Ahmet YILDIRIM -- 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

[gmx-users] Regarding 1-d free energy profile from g_sham

Hello, I am using g_sham to plot a one dimensional free energy profile for a given reaction coordinate( in my case it is first principal component(PC1) from a principal component analysis). It gives me the bin index Vs free energy plot, but I want PC's value Vs free energy plot. Please suggest me

[gmx-users] analyzing protein conformation stability

Hello Dear users is there any command in gromacs for analysis of protein stability? or I should be using those related to calculation of B-factor? best regards, sajad-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

[gmx-users] About the GROMOS96 parameters files

Dear GMXusers, I would like to reproduce the results obtained in the paper of Marrink et al "Molecular dynamics simulations of the kinetics of spontaneous micelle formation". J. Phys. Chem. B, 104:12165-12173, 2000". In this (old but interesting) work, the authors used the GROMOS96 force field t