[gmx-users] Re: window exchange umbrella sampling

[Michael Shirts]

4.5.7 does not support Hamiltonian exchange.  It says all properties
are the same, because all the temperatures and pressures are the same
-- it won't switch the umbrellas.

On Wed, Jul 17, 2013 at 3:30 PM, Parisa <akhshi.pa at gmail.com> wrote:
> Hi Michael,
>
> I think that this is an issue with the gromacs version I am using (4.6.1). I
> switched to 4.5.7 and now, I get the error:
>
> Fatal error:
> The properties of the ... systems are all the same, there is nothing to
> exchange
>
> I don't understand what I am missing here. I suppose if I have 3 replicas to
> fix a molecule at positions 1.0 and 2.0 and 3.0 while the force constant is
> being exchanged between them in a range of 300 to 200, I can define 3 mdp
> files as below:
>
> For replica 1 at position 1.0:
>
> 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 1.0
> 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
>
> For replica 2 at position 2.0:
>
> 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 2.0
> pull_rate1               = 0
> pull_k1                  = 300
> pull_kB1                 = 200
> free_energy              = yes
> restraint-lambdas  =  1.0 0.5 0.0
> init-lambda-state   =  1
> nstdhdl             = 10
>
> For replica 3 at position 3.0:
>
> 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 3.0
> pull_rate1               = 0
> pull_k1                  = 300
> pull_kB1                 = 200
> free_energy              = yes
> restraint-lambdas  =  1.0 0.5 0.0
> init-lambda-state   =  2
> nstdhdl             = 10
>
> Could you please comment if I am missing something here? Unfortunately,
> there is not much about this posted before.
>
> Many thanks,
>
> Parisa
>
>
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> --
> View this message in context: http://gromacs.5086.x6.nabble.com/window-exchange-umbrella-sampling-tp5009894p5009947.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
> --
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