Re: [gmx-users] How to obtain structures with large RMSD?

you either A) Have not been sampling long enough or B) Just might have your answer... On Oct 10, 2011, at 11:46 AM, Liu, Liang wrote: Well, the thing is even I turn off the position restraint and raise the temperature to 600k, the RMSD I can obtained is only about 0.3 for a RNA hairpin. -

Re: [gmx-users] How to obtain structures with large RMSD?

Well, the thing is even I turn off the position restraint and raise the temperature to 600k, the RMSD I can obtained is only about 0.3 for a RNA hairpin. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.

Re: [gmx-users] How to obtain structures with large RMSD?

Well, I am only trying to get structures with some of them far from the initial structure (large RMSD) and some of them close to the initial one... On Mon, Oct 10, 2011 at 10:37 AM, Tsjerk Wassenaar wrote: > Hi Liang Liu, > > You will never get broader sampling by adding restraints. If you want >

Re: [gmx-users] How to obtain structures with large RMSD?

Liu, Liang wrote: How's position restraint? If the force constant is reduced (reduce the number in posre.itp ?), the simulation will lead to more flexible structure? Position restraints are inherent inhibition to structural sampling. Their intent is to prevent the protein (or whatever res

Re: [gmx-users] How to obtain structures with large RMSD?

Hi Liang Liu, You will never get broader sampling by adding restraints. If you want to have broader sampling, raise the temperature or add denaturants. But also ask yourself the question if what you think you want is what you should be wanting. What is the actual question you're trying to solve?

Re: [gmx-users] How to obtain structures with large RMSD?

How's position restraint? If the force constant is reduced (reduce the number in posre.itp ?), the simulation will lead to more flexible structure? On Mon, Oct 10, 2011 at 10:20 AM, Justin A. Lemkul wrote: > > > Liu, Liang wrote: > >> Thanks. >> >> Will the constrain help? >> >> > Bond constrain

Re: [gmx-users] How to obtain structures with large RMSD?

Tsjerk Wassenaar wrote: Hey Justin, Large RMSD values would indicate non-native structures, which doesn't sound like what you're looking for. If your goal is simply enhanced sampling, try REMD. I think this is put too boldly. There are plenty of examples where pairs from native ensembles ha

Re: [gmx-users] How to obtain structures with large RMSD?

Hey Justin, > Large RMSD values would indicate non-native structures, which doesn't sound > like what you're looking for.  If your goal is simply enhanced sampling, try > REMD. I think this is put too boldly. There are plenty of examples where pairs from native ensembles have large RMSD: e.g., pro

Re: [gmx-users] How to obtain structures with large RMSD?

Liu, Liang wrote: Thanks. Will the constrain help? Bond constraints? Well, in general, they're useful, and likely necessary at high temperature to keep your system stable. Please be more specific. -Justin On Mon, Oct 10, 2011 at 10:06 AM, Justin A. Lemkul > wro

Re: [gmx-users] How to obtain structures with large RMSD?

Thanks. Will the constrain help? On Mon, Oct 10, 2011 at 10:06 AM, Justin A. Lemkul wrote: > > > Liu, Liang wrote: > >> Hi, all, >> >> I am trying to use Gromacs to obtain structural ensembles around native >> structures (PDB structures). >> However the simulated structures are always very clos

Re: [gmx-users] How to obtain structures with large RMSD?

Liu, Liang wrote: Hi, all, I am trying to use Gromacs to obtain structural ensembles around native structures (PDB structures). However the simulated structures are always very close to the initial one, with RMSD < 0.2. I am wondering how to obtain large-RMSD structures? Thanks. Large RM

[gmx-users] How to obtain structures with large RMSD?

Hi, all, I am trying to use Gromacs to obtain structural ensembles around native structures (PDB structures). However the simulated structures are always very close to the initial one, with RMSD < 0.2. I am wondering how to obtain large-RMSD structures? Thanks. -- Best, Liang Liu -- gmx-users m