[gmx-users] Fwd: Last step before CG em.mdp

[Francesco Pietra]

On Mon, Nov 30, 2009 at 8:18 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> Francesco Pietra wrote:
>>
>> Failed to specify that both the DPPC bilayer and the box of water are
>> from equilibrated systems in MARTIN web, while the protein was Amber
>> minimized (and MD) before generating the CG.
>>
>> I have tried the cg protein alone
>>
>> genbox -cp my.pdb -box 15 -o my.gro
>>
>
> Again I ask why you are using SPC as the solvent.  If you indeed want to use
> the MARTINI CG water representation, you must pass its configuration
> explicitly to the -cs flag.  Otherwise, the default (spc216.gro) is used.

The water that I set around the extracellular part of the protein was
equilibrated cg water (by just multiplying the box furnished on
MARTINI). In relation to the command above, I don't understand your
remark, simply because there is no water at all, both in the input
.pdb and output.gro. This is true for my previous post, too.


>
> Are you defining the protein's position in the box before solvation?  Using
> editconf -c is your friend.

I did present work before getting your mail. Curiously, gmail now
places your mail in spam. Luckily I noticed that.
A point I have to pay much attention to - for a possible major mistake
in my procedure - is your "before solvation". I assumed no solvation
at all.



>
>> grompp -f em.mdp -c my.gro -p my.top -o topol.tpr
>>
>> mdrun -v -s topol.tpr
>>
>> steepest descents converged to machine precision but not to the
>> requested Fmax < 2000
>>
>> Pot Ener 7.1e+08
>> Max force 6.1e+10 on atom 983
>> Norm of force 2.5e+11
>>
>> confout.gro shows that one of the subunits has been displaced from the
>> multimer (apparently both intact) There is a long bond between the
>> displaced subunit and the rest of the multimer, very closely to the
>> atom 983 of max force, located in the pore region. I have scarce
>> experience with gromacs yet, hope that this suggests remedies. I used
>> a crude version of em.mdp.
>>
>
> Well, there are several potential problems.  One is the box size (as I
> mentioned in my last message).  The other question is whether or not the
> conversion from atomistic to CG was done correctly.  I know I have mentioned
> the problems with the MARTINI script a number of times, and perhaps this has
> also come up in our discussions before, but do check that the starting CG
> coordinates make sense.

The cg protein model superimposes nicely to the full-atom model. The
dimensions I gave in my previous mail were DPPC and W inclusive but
"-box 15" is still to small. The protein might have seen its neighbor.

>
> Beyond that, try an in vacuo minimization of your protein and see what
> happens there.

Do you mean without setting "-box"? I got confused about that, I
thought to have vacum around the protein (or the protein+DPPC+W of
previous mail) with

 genbox -cp my.pdb -box 15 -o my.gro


I'll try tomorrow to implement all your suggestions. Thanks a lot
francesco

>
> -Justin
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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