[gmx-users] LIE method

Mahboobeh Eslami mahboobeh.eslami at yahoo.com
Fri May 30 08:22:40 CEST 2014

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 A. Lemkul, Ph.D.
Postdoctoral Fellow

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

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

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