[gmx-developers] Free energy calculations in 3.3_rc1

[Erik Lindahl]

Hi David,

Apart from the PME free energy loops we now use lambda instead of  
lambda^2 by default in the softcore interpolation. According to Berk  
this results in less noise, and he's usually right :-)

You can control it with the parameter sc_power - use 2 to imitate the  
behavior of previous gromacs versions.

(I think it should be documented in share/html/online/mdp_opt.html too).

Cheers,

Erik

On Sep 9, 2005, at 11:33 AM, David Evans wrote:

> Hi,
>
> I just tested the (single processor) 3.3_rc1 version on one
> of my systems, involving perturbing a ligand in water.
> I compared the results to those from identical input
> files run with a CVS version checked out on 23/11/2004.
> I have been experimenting with this CVS version for a while,
> since I believed it to include free-energy PME loops (see previous  
> postings
> on this list).
>
> I found significantly (100 kJ) different values of dg/dl between  
> the two versions,
> although when you integrate across lambda the sums differ by only  
> 1-2 kJ
> (which is still significant according to my error analysis, but not  
> by much).
> Does anyone knows why this is, and whether the 3.3_rc1 version
> is likely to be more accurate? My .mdp file is below, and I can  
> provide
> any more details anyone needs.
>
> Thanks,
>
> Dave
>
> cpp                 =  /lib/cpp
> ;define              =  -DFLEX_SPC
> integrator          =  md
> nsteps              =  1000000
> dt                  =  0.002
>
> comm_mode           = linear
> nstcomm             = 1000
> comm_grps           = system
>
> nstxout             = 500000
> nstvout             = 500000
> nstlog              = 100
> nstenergy           = 100
> nstxtcout           = 2000
>
> tcoupl              = nose-hoover
> tc_grps             = system
> tau_t               = 1
> ref_t               = 300
> gen_vel             = yes
> gen_temp            = 300
>
> pcoupl              = berendsen
> pcoupltype          = isotropic
> tau_p               = 1
> ref_p               = 1
> compressibility     = 4.46e-5
>
> constraints         = hbonds
> constraint_algorithm = lincs
>
> coulombtype         = PME
> rvdw                = 0.9
> rlist               = 0.9
> rcoulomb            = 0.9
> fourierspacing      = 0.12
> pme_order           = 4
> ewald_rtol          = 1e-5
>
> vdwtype         = cut-off
> pbc                 = xyz
> dispcorr            = enerpres
>
> free_energy  = yes
> init_lambda = 0.1
> sc_alpha  = 1.0
>
> --
> David Evans
> School of Pharmacy
> University of London
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