[gmx-users] window exchange umbrella sampling
mrshirts at gmail.com
Tue Jul 16 23:02:58 CEST 2013
You need to have different pull parameters at the end states. Right
now, pull-kB1 is not defined in your code, so there is nothing to
interpolate to: it assume pull-kB1 = pull-k1.
Longer scale -- one would want to define reference distances that
change with lambda within the same simulation, but looking over the
code, I'm not seeing anything. One would want to add a pull_vect1B to
change the location of the restraint as a function of lambda, but this
isn't yet defined. That should be something we look at in the future
. . .
On Tue, Jul 16, 2013 at 2:41 PM, Parisa Akhshi <akhshi.pa at gmail.com> wrote:
> I am trying to use Hamiltonian replica exchange as implemented in Gromacs.
> The idea is to use different pulling umbrella forces and then obtain a PMF
> profile. I am specifically interested in exchanging force constants between
> To do a quick test, I successfully ran replica exchange in which the
> temperature is exchanged. In this case, I prepared for example 8 tpr files
> at 8 different temperatures and run them using
> mpirun -np 8 mdrun_mpi -s prefix_.tpr -multi 8 -replex 100
> And it ran just fine.
> For window exchange umbrella sampling, though, I am confused with the input
> preparation. I am not sure how to specify in the .mdp file how the values
> of pull force should be used to define different force constants for
> different replicas. Also, when submitting the job, how should I ask the
> program to exchange pull forces between windows? I tried using this:
> But, it gives me the error:
> Fatal error:
> The properties of the ... systems are all the same, there is nothing to
> I noticed a previous discussion on below link:
> However, I am not sure how to use the restraint-lambda parameter exactly.
> Is there any example, ... how to use it?
> I have copied the related portion of one of the the .mdp files below for
> moving MOL2 with respect to MOL1
> Thanks for your help,
> pull_group0 = MOL1
> pull_weights0 =
> pull_pbcatom0 = 0
> pull_group1 = MOL2
> pull_weights1 =
> pull_pbcatom1 = 0
> pull_vec1 = 0.0 0.0 0.0
> pull_init1 = 0.0 0.0 0.0
> pull_rate1 = 0
> pull_k1 = 300
> free_energy = yes
> restraint-lambdas = 0.0 0.5 1.0 0.0 0.5 1.0 0.0 0.5 1.0
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