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

[Da-Wei Li]

Well. It  actually isn't dead but becomes very slow for large proteins.
dawei

On Mon, Feb 7, 2011 at 11:44 AM, Da-Wei Li <lidawei at gmail.com> wrote:

> 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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