[gmx-users] Energy minimization problem after editconf step

[Justin Lemkul]

On 9/2/14, 10:49 AM, neha bharti wrote:
> Thanks for your reply Justin
>
> The error is now solve but I don't know this is a right way or not.
>
>
> The step which I perform previously in which I am facing error:
>
> Packing :
>
> 1) perl inflategro.pl em.gro 0.95 POPC 0 system_shrink1.gro 5
> area_shrink1.dat
>
> 2) grompp -f em.mdp -c system_shrink1.gro -p topol.top -o em.tpr
>
> 3) mdrun -v -deffnm em
>
> I did this till 24 iteration then I reached area per lipid 0.70 nm^2
>
>
>
> 4) Adding Solvent:
>
> a) editconf -f system_shrink.gro -o POPC_box.gro -box 8.68740 8.41864
> 12.70145
>
> b) genbox -cp  POPC_box.gro -cs spc216.gro -o  POPC_sol.gro
>
>
>
> 5) Adding Ions
>
> a) grompp -f ion.mdp -c POPC_sol.gro -p topol.top -o ion.tpr
>
> b) genion -s ion.tpr -o POPC_sol_ions.gro -p topol.top -pname NA -np 1
> -nname CL
>
> Select 16 to add 1 possitive ion to sol
>
>
>
> 6) Energy Minimization
>
> Next, energy minimize the entire system now, using the following commands:
>
> a) grompp -f em.mdp -c POPC_sol_ions.gro -p topol.top -o em.tpr
>
> b) mdrun -v -deffnm em
>
>
>
> In energy minimization step
> The following error occur
>
> Steepest Descents converged to machine precision in 18 steps,
>   but did not reach the requested Fmax < 1000.
>   Potential Energy  =  6.1499341e+20
>   Maximum force     =            inf on atom 3300
> Norm of force     =  5.4206209e+1
>
> But if I skip the editconf step 4(a) the the energy minimization is normal.
> But i need to increase the box size because my protein is out of the box.
>
>
> So I did some changes before the packing which gives the correct result.
> The steps are as follows:
>
>
> Before energy minimization of POPC.gro I remove the water (SOL molecule
> manually) then increase the box size by
>
> 1) editconf -f POPC.gro -o popc_new.gro -box 8.68740 8.41864 15 : With the
> help of this command I increase the box size of popc.gro which I have
> downloaded. ( Peter C. Lai POPC lipid http://cesium.hyperfine.info/~peter
> /gromacs/popc36/ )
>
>
> 2) genbox -cp  POPC_new.gro -cs spc216.gro -o  POPC_new_sol.gro : Add
> solvent
>
>
> 3) Energy minimization:
> a) grompp -f em.mdp -c POPC_new_sol.gro -p topol_popc.top -o em.tpr
> b) mdrun -v -deffnm em
>
> 4) trjconv to remove periodicity:
>
> trjconv -s em.tpr -f em.gro -o popc_whole.gro -pbc mol -ur compact
>
> select 0 for system
>
> orient the KALP peptide within this same coordinate frame as popc_whole.gro
>
> editconf -f conf.gro -o conf_newbox.gro -c -box 8.68740 8.41864 12.70145
>
> Rest of the step is same as above after packing I took system_shrink24.gro
> without using editconf because I already arrange the size of the box like
>
>   Adding Solvent:
>
> a) genbox -cp  system_shrink24.gro -cs spc216.gro -o  POPC_sol.gro
>
>
>
>   Adding Ions
>
> a) grompp -f ion.mdp -c POPC_sol.gro -p topol.top -o ion.tpr
>
> b) genion -s ion.tpr -o POPC_sol_ions.gro -p topol.top -pname NA -np 1
> -nname CL
>
> Select 16 to add 1 possitive ion to sol
>
>
>
> 6) Energy Minimization
>
> Next, energy minimize the entire system now, using the following commands:
>
> a) grompp -f em.mdp -c POPC_sol_ions.gro -p topol.top -o em.tpr
>
> b) mdrun -v -deffnm em
>
>
> When I perform by above method my energy minimization occur.
> Is this the right way??
>

If it works, you can't argue with results.  I don't know why the first method 
didn't work, but it appears you've found a solution.

-Justin

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

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA 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
http://mackerell.umaryland.edu/~jalemkul

==================================================