[gmx-users] Re: window exchange umbrella sampling

[Parisa]

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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