Re: [gmx-users] probability distribution of bond distance/length

On Fri, Nov 1, 2013 at 4:04 AM, Xu Dong Huang wrote: > Dear all, > > I would like to assess the probability distribution of particle bond > distance/length over the entire run, specifically I want to collect > possibly a histogram representation or even a regular plot. Would using > g_bond be the

Re: [gmx-users] GMX manually generate topology for residues

They're http://en.wikipedia.org/wiki/C_preprocessor symbols that are #defined elsewhere in the directory that contains that .rtp file. The names/symbols probably map to the original force field literature. grep is your friend. Mark On Fri, Nov 1, 2013 at 6:45 AM, charles wrote: > i am a newbie

[gmx-users] ligand-protein simulation

Dear all gromacs users, I have run a protein-ligand simulations. However, the position of the ligand is not reasonable after 10ns simulation. There is no problem with the force field paramers of the ligand. I am trying to constrict the ligand move for 500ps simulation. But i do not know whethe

[gmx-users] Lysozyme in Water at different pH and Ionic strength

Dear Gromacs users, Just was wondering if it is possible to protein solution let say Lysozyme in Water example of Justin tutorial at different pH and ionic strengths, if so how? Thanks -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please

Re:[gmx-users] Lysozyme in Water at different pH and Ionic strength

It is impossible. But you can add proton to the acidic amino acid. At 2013-11-01 20:36:41,Mass wrote: >Dear Gromacs users, >Just was wondering if it is possible to protein solution let say Lysozyme in >Water example of Justin tutorial at different pH and ionic strengths, if so >how? >Thanks

Re: [gmx-users] ligand-protein simulation

On 11/1/13 5:37 AM, xiao wrote: Dear all gromacs users, I have run a protein-ligand simulations. However, the position of the ligand is not reasonable after 10ns simulation. There is no problem with the force field paramers of the ligand. I am trying to constrict the ligand move for 500ps simu

Re: [gmx-users] Lysozyme in Water at different pH and Ionic strength

On 11/1/13 8:39 AM, xiao wrote: It is impossible. But you can add proton to the acidic amino acid. It's certainly not impossible. There are constant-pH methods that exist; the list archive contains many posts on this topic, and more information can be found at: http://www.gromacs.org/Do

Re: [gmx-users] Lysozyme in Water at different pH and Ionic strength

Following up on Justin's reply I just want to add that, not only is it possible, as it has been done before. For instance: http://www.ncbi.nlm.nih.gov/pubmed/18214978 http://www.ncbi.nlm.nih.gov/pubmed/22072522 Luís Filipe ITQB-UNL, Portugal 2013/11/1 Justin Lemkul > > > On 11/1/13 8:39 AM, xi

Re: [gmx-users] Lysozyme in Water at different pH and Ionic strength

I notice that both papers mention modifications to GROMACS and cite the following: http://www.ncbi.nlm.nih.gov/pubmed/16471903 > Following up on Justin's reply I just want to add that, not only is it > possible, as it has been done before. For instance: > > http://www.ncbi.nlm.nih.gov/pubmed/18214

Re:Re: [gmx-users] ligand-protein simulation

Hi Justin, Thank you very much for your response. I used GAFF force field parameters for the ligand. I have done another short MD simulation, and this time everything seems fine, so i have no idea where the problem is from. Best wishes Fugui At 2013-11-01 20:41:46,"Justin Lemkul" wrote:

[gmx-users] Gibbs Energy Calculation and charges

Dear Dallas: Seems like you could test Michael's idea by removing all 1-4 NB interactions from your topology. It won't produce any biologically useful results, but might be a worthwhile check to see if indeed this is the issue. To do this, I figure you would set gen-pairs to "no" in the [ defau

[gmx-users] Re: Hardware for best gromacs performance?

Im not sure on the prices of these systems any more, they are getting dated so they will be on the low end price wise. I have a 30,000 ish atom lipid system for all my simulations so this might be helpful: System 1 CPU - dual 6 core xeon @ 2.8 GHz GPU - 2x GTX 680 50 ns/day System 2 CPU - dual 4

[gmx-users] ligand problem

Hi gmx-users I prepared the DNA topology by using the parmbsc0 force field. I want to apply the GAFF force field for the ligand by using the antechamber module of ambertools13. I optimized my ligand by Gaussian program at B3lyp/6-31G* in solvent (water) phase, but I don't know how to calculate R

[gmx-users] Re: Hardware for best gromacs performance?

Have you used/considered any cloud approaches? -- View this message in context: http://gromacs.5086.x6.nabble.com/Hardware-for-best-gromacs-performance-tp5012124p5012154.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org

[gmx-users] g_lie and ligand only simulation

Dear Gromacs users, I have a protein-ligand in water simulation (Gmx 4.5.3), for calculating free energy of ligand binding, a separate simulation of ligand in water simulation is required (which I read from the list). The question is the protein-ligand is simulated as a dimeric system so is it nec

[gmx-users] g_lie and ligand only simulation

Dear Users, Its mentioned in the list that it would be wrong to use g_lie on a simulation which uses PME. So kindly suggest any other way available to get the free energy of ligand binding other using g_lie? Thank you Regards kavya -- gmx-users mailing listgmx-users@gromacs.org http://lists