[gmx-users] H-REMD in umbrella sampling

adam adam.orlowski at ul.ie
Tue Nov 24 18:06:43 CET 2015


Thank you for the advice.
Though, I am a bit confused how one could implement such particles in practice. What do you understand by “make two virtual particles” ? Where it should be defined in gromacs inputs ? 

Also, as I understand, if I run standard umbrella sampling simulation with the pulling code in gromacs, it is already using such approach (COM pulling). I suppose that the issue here is how to force gromacs to treat different distances between COMs (and therefore different pulling potential leading to different Hamiltonian) as an argument for REMD (H-REMD in this case) and perform exchange between the umbrella windows.

Since there is no answer from gromacs developers I assume that the above is not yet implemented and based on the http://redmine.gromacs.org/issues/1335 <http://redmine.gromacs.org/issues/1335> the implementation is postponed for the “future”. Thus, anyone trying to use such feature should look for solution elsewhere.

Thank you.

Best regards,

> On 23 Nov 2015, at 17:12, Yuri Garmay <yuri.from.spb at gmail.com> wrote:
> One can make two virtual particles at COMs of corresponding molecules
> and set harmonic potential between them with different length for
> lambdas 0 and 1.
> -- 
> Best regards,
> Yuri
> -- 
> Gromacs Users mailing list
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.

More information about the gromacs.org_gmx-users mailing list