[gmx-users] Re: window exchange umbrella sampling

[Michael Shirts]

Ah, this is a force field issue -- urey-bradley terms are not
supported free energy calculations. However, since only restraints are
changing, this warning doesn't really need to be there.

It would be relatively simple to put in a check to allow this to work,
but it might take a week or two to get around to it.

I'll file a redmine in the meantime, in case someone else can get to it first!

http://redmine.gromacs.org/issues/1302



On Tue, Jul 16, 2013 at 5:32 PM, Parisa <akhshi.pa at gmail.com> wrote:
> Thanks for quick reply. I fixed the issue with kB1. Below is what I have
> changed in the .mdp file. I use this to run it "mpirun -np 3  mdrun_mpi -s
> prefix_.tpr -multi 3 -replex 6 -dhdl a.dhdl". But I get this error (I am
> using version 4.6.1):
>
> Fatal error:
> Function type U-B not implemented in ip_pert
> For more information and tips for troubleshooting, please check the GROMACS
>
> Here is the input file:
> .
> .
> .
> pull_group0              = POPC
> pull_weights0            =
> pull_pbcatom0            = 0
> pull_group1              = DNA
> 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
> pull_kB1                 = 200
>
> free_energy              = yes
> restraint-lambdas  =  1.0 0.5 0.0
> init-lambda-state   =  0
> nstdhdl             = 10
> .
> .
> .
>
> Any idea about it?
>
> Thanks,
>
> Parisa
>
>
>
>
> --
> View this message in context: http://gromacs.5086.x6.nabble.com/window-exchange-umbrella-sampling-tp5009894p5009899.html
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