[gmx-users] LIE method

[Mahboobeh Eslami]

hi
dear justin
A few months ago I asked you a question about LIE method. 
According to your guide, i wrote a new .mdp file that didn't use PME (I used RF) and used following command for protein-ligand complex  and ligand-sol simulations:
 mdrun -s newtpr.tpr -rerun full20ns.xtc
 then I extract -Elj and -Eqq of ligand in water simulation and use g_lie command.
But the obtained free energy has great difference with the experimental value.

You told me that i must re-calculate energies from  PME systems, then i must take the difference of the energies from another system where the same correction hasn't been applied.
Please explain this. How do I do it?
I have urgent need to calculate the free energy.
Thank you sincerely




On Monday, January 13, 2014 5:22 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
 




On 1/12/14, 5:18 PM, Mahboobeh Eslami wrote:
> dear Justin thanks a lot
> I use Amber03 force field and TIP3P water model for my system. following options
> are used in first my mdp file:
> nstlist  = 5
> rlist  = 1.0
> rcoulomb = 1.0
> rvdw  = 1.0
> I have following questions. if possible, please answer them.
> 1) are these options good for LIE method? do LIE method need especial options?

Run settings like these are dependent upon the force field.  LIE is simply a 
post-processing technique.

> 2) I saw following advice in gmx forum " save a lot of frames to get reasonably
> accurate numbers " (http://gromacs.5086.x6.nabble.com/PME-td4450969.html)
> do you have especial comment for frame saving?

No insight there.  I am not familiar with the details of what was proposed in 
that post.  As far as I know, most people do not attempt to re-figure energies 
like that; they simply re-process using RF or long cutoffs (RF is better).

> 3)  I use *coulombtype = *cutoff  and rcoulomb = 1.0 in new mdp file for
> rerun energies. are these options good or not?

No, plain cutoffs are very inaccurate.


-Justin

-- 
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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
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Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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