[gmx-users] LIE method

[Mahboobeh Eslami]

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



On Sunday, January 12, 2014 8:36 PM, Mahboobeh Eslami <mahboobeh.eslami at yahoo.com> wrote:
  
dear justin
I sincerely thank you for your answer my questions
I saw the following description for tpbconv command in the gromacs manual:
"by setting the charges of a specified group to zero. This is
 useful when doing free energy estimates using the LIE (Linear Interaction Energy) method".
I do not know how to use this command.I think that this command is used only for charged ligand. is this correct?
Thanks and best wishes




On Sunday, January 12, 2014 7:19 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
  


On 1/12/14, 12:03 AM, Mahboobeh Eslami wrote:
> dear Justin thanks for your reply
> is the rerun energies needed only
for protein ligand complex? do the ligand in
> water simulation need the rerun energies?

Both.  It wouldn't make sense to re-calculate energies from one
 PME system, then 
try to take the difference of the energies from another system where the same 
correction hasn't been applied.

-Justin

> thanks a lot
>
>
> On Sunday, January 12, 2014 1:11 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 1/11/14, 2:07 AM, Mahboobeh Eslami wrote:
>  > hi dear GMX users
>  > I simulated protein-ligand complex for 20 nanoseconds. I want to calculate
> free energy by LIE method so I simulated ligand in water in the same conditions.
> I used PME and full periodic boundary conditions in my simulations so I wrote a
> new .mdp file that didn't use PME (I used cut off) and used following command
> for protein-ligand complex simulation:
>  > mdrun -s newtpr.tpr -rerun full20ns.xtc
>  > then I extract -Elj and -Eqq of ligand in water simulation and use g_lie command.
>  > are these steps sufficient. is the stage or another commandnecessary?
>
>
> If the protein-ligand simulation was done with PME as well, then you need to get
> the rerun energies, as well.
>
> -Justin
>
> --
>
==================================================
>
> 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 <mailto:jalemkul at outerbanks.umaryland.edu> |
> (410) 706-7441

>
>
> ==================================================
>
>

-- 
==================================================

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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