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

[TJ Mustard]

Dawei,

 

I have no problems with proteins in the thousands of atoms. Can you post your command line and mdp files?

 

Thank you,

TJ Mustard 

On February 7, 2011 at 9:31 AM Da-Wei Li <lida...@gmail.com> wrote:

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 <lida...@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 <lida...@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

 

TJ Mustard
Email: musta...@onid.orst.edu

-- 
gmx-users mailing list    gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists