Thank you so much!
But I have a new problem as follows:
<<
Running multisander version of sander Amber12
Total processors = 4
Number of groups = 2
[cli_0]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
[cli_2]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 2
rank 0 in job 230 localhost_39799 caused collective abort of all ranks
exit status of rank 0: return code 1
>>
I used 4 cpus to run sander.MPI
On Mon, Sep 30, 2013 at 8:01 PM, David A Case <case.biomaps.rutgers.edu>wrote:
> On Mon, Sep 30, 2013, 冉挺 wrote:
>
> > I read the tutorial that's "Thermodynamic Integration using soft
> core
> > potentials
>
> > I want to modeling the water contribution to the ligand-binding affinity
> by
> > the double decoupling method.
>
> It's not clear what you mean by the "water contribution to the ligand
> binding
> affinity". A "standard" simulation of the ligand binding free energy will
> automatically include the effects of the solvent.
>
> > I wonder if the icfe parameter should be set from minimization
> > mdin to equilibrium mdin
>
> You would ordinarily use the same icfe value at all steps. Note that
> minimization is often not needed.
>
> > if the water should be constraint at the
> > binding site by a constraint force as described in the literature
>
> You would ordinarily not constraint solvent molecules. But note that it
> may
> take a long time to equilibrate if there are trapped waters.
>
> > As well, I cannot use the pmemd method to run Thermodynamic Integration
>
> This is correct; the next release of pmemd will have this feature.
>
> > My command is "sander -ng 2 -groupfiles 《Mygroupfiles》"
> > the erro is "mdfil: Error unknown flag: -ng" but the recommended
> > parameters include the -ng flag. I used amber10.
>
> You must use sander.MPI (not sander), and the corresponding mpirun command
> to
> carry out thermodynamic integration calculations.
>
> Since you seem to be very new to this, be sure to get familiar with small
> and
> "easy" transformations before attempting something difficult.
>
> ...good luck...dac
>
>
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>
--
PhD Ting Ran
CPU(CHINA PHARMACEUTICAL UNIVERSITY)
Molecular-Design & Drug-Discovery Lab
Laboratory Building A212
639 Longmian Avenue
Nanjing, 210009
P.R.China
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Received on Mon Sep 30 2013 - 06:30:04 PDT
