[gmx-users] Re: free energy calculation , grompp crash

[Da-Wei Li]

hi,

I did more test and found that it depended on size of the protein. Grompp
will die when number of atoms of the protein is larger than about 200. Is it
possible the source code limit the size of the protein that can be
decoupled?

thanks.


dawei

On Mon, Feb 7, 2011 at 10:34 AM, Da-Wei Li <lidawei at gmail.com> wrote:

> Dear users
>
> I tried free energy calculation but grompp couldn't go through. It stops
> after
>
> *******************
> Generated 2278 of the 2278 non-bonded parameter combinations
> Generating 1-4 interactions: fudge = 0.5
> Generated 2278 of the 2278 1-4 parameter combinations
> Excluding 3 bonded neighbours molecule type 'Protein'
> turning H bonds into constraints...
> Excluding 2 bonded neighbours molecule type 'SOL'
> turning H bonds into constraints...
> Excluding 1 bonded neighbours molecule type 'CL'
> turning H bonds into constraints...
> Coupling 1 copies of molecule type 'Protein'
> *******************
>
> The CPU usage is 100%.
>
> I just add following into the mdp file:
>
> ***************
> free_energy              = yes
> init_lambda              = 0.0
> delta_lambda             = 0
> sc_alpha                 =0.5
> sc-power                 =1.0
> sc-sigma                 = 0.3
> couple-moltype           = Protein
> couple-lambda0           = vdw-q
> couple-lambda1           = none
> ***************
>
> Does anyone have some idea about this problem?  thanks.
>
> Another question is whether I can switch off "two molecules" (such as
> protein+ligand) in free energy calculation? I searched this list and got
> that 4.0.7 did support this. how about 4.5.4?
>
> dawei
>
>
>
>
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