[gmx-users] Energy minimization problem after editconf step

[neha bharti]

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??

Thanks

With Regards

Neha bharty




> > Hello All
>>
>>  I am trying to perform MD for protein ligand complex in popc lipid with
>>  Charmm36 force field. I follow Justin A. Lemkul tutorial of membrane
>>  protein simulation.
>>
> > I have successfully perform till InflateGRO followed by energy
minimization
> > step.
>>
> > perl inflategro.pl em.gro 0.95 POPC 0 system_shrink1.gro 5
area_shrink1.dat
>>
> >   grompp -f em.mdp -c system_shrink1.gro -p topol.top -o em.tpr
>>
>>  mdrun -v -deffnm em
>>
> > till 24 iteration then I reached area per lipid 0.70 nm^2
>>
>>  when I visualize the molecule then the box size small in Z axis so in
>>  editconf step I increase the box size and then add solvent and ion .
when I
>>  increase the box size with editconf then there is atomic clashes
occur.and
>>  giving following error:
>>
>>  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
>
>>
>>   When I skip this step (editconf) then the minimization is normal.
>> But I need to increase the box size.
>> How to increase the box size?
>

>You need to provide the exact commands that you used when manipulating the
box,
>otherwise it's pure guesswork.