Re: [gmx-users] Re: gb_saltconc in implicit water simulations

2010-12-22 Thread Per Larsson
Hi! Which results can you not recreate? Yes - all simulations were run at zero salt concentration. Implicitly this means that we did not do anything special to treat the charges. The protein has an overall charge of -2, looking at the topology. In hindsight, we probably should have given this i

Re: [gmx-users] Re: gb_saltconc in implicit water simulations

2010-12-21 Thread Rogan Carr
Hi Per (and all), I am trying to recreate the results of the CHARMM forcefield implementation to better understand how to implement implicit solvent models, but I can't quite recreate your results. If the Gromacs code doesn't use salt concentrations, does that mean that your simulations

Re: [gmx-users] Re: gb_saltconc in implicit water simulations

2010-12-14 Thread Per Larsson
Hi! Sorry that I missed this discussion, we recently moved the lab and there where quite many things to attend to. When we did the implementation of implicit solvent into Gromacs, one of the strong points was to see how fast we could make it, to speed up conformational sampling as much as poss

Re: [gmx-users] Re: gb_saltconc in implicit water simulations

2010-12-14 Thread devicerandom
On 14/12/10 19:04, Justin A. Lemkul wrote: I was going to send a very similar mail -namely, I have a coarse-grain system in vacuum where I'd like to simulate a charged polymer. My idea was that of adding a single "ghost" counter-ion with zero VdW interactions, perhaps keeping it fixed in one corn

Re: [gmx-users] Re: gb_saltconc in implicit water simulations

2010-12-14 Thread Justin A. Lemkul
devicerandom wrote: On 14/12/10 18:35, Bob Johnson wrote: Can anyone answer this question or guide me somewhere with helpful information? Thanks, Bob I was going to send a very similar mail -namely, I have a coarse-grain system in vacuum where I'd like to simulate a charged polymer. My idea

Re: [gmx-users] Re: gb_saltconc in implicit water simulations

2010-12-14 Thread devicerandom
On 14/12/10 18:35, Bob Johnson wrote: Can anyone answer this question or guide me somewhere with helpful information? Thanks, Bob I was going to send a very similar mail -namely, I have a coarse-grain system in vacuum where I'd like to simulate a charged polymer. My idea was that of adding a

[gmx-users] Re: gb_saltconc in implicit water simulations

2010-12-14 Thread Bob Johnson
Can anyone answer this question or guide me somewhere with helpful information? Thanks, Bob On Thu, Dec 9, 2010 at 4:52 PM, Bob Johnson wrote: > Hello everyone, > I am trying to use implicit solvent with a CG DNA model. The model, > however, uses explicit charges, which means that the DNA carries