[gmx-users] Decomposition in minimization step

[Mark Abraham]

Hi,

> Thank you so much for paying attention to my question. but as I said
before I have problem in minimization step. the structure of my ligand is
broken after this step, so I couldn't use the em.gro for the next
equilibration step (NVT and NPT) before the main MD run simulation.
Actually I don't know what the problem is?
how can I fix this problem ?

Please leave the discussion on the list, so others can contribute and
others can also learn. There are an infinite number of equivalent
representations of your system, and mdrun doesn't take the time to guess
which one of them you'd prefer to have in the output. However, if you for
example like the one that you used as input to grompp, then you might do

gmx grompp -f preferred
gmx mdrun -c broken
gmx trjconv -s preferred -f broken -pbc whole

or perhaps other things that are suggested on the page I linked.

Mark

On Tue, Jul 12, 2016 at 4:40 PM Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> mdrun can't know what your visualization preference will be, and then VMD
> doesn't know how to guess either. See
> http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions for
> tips.
>
> Mark
>
> On Tue, Jul 12, 2016 at 4:35 PM Yeganeh Entezari <
> yeganeh.entezari at gmail.com> wrote:
>
>> Hi,
>> I have a problem after this step:
>>
>> grompp -f em.mdp -c sol_ions.gro -p topol.top -o em.tpr
>> mdrun -v -deffnm  em
>>
>>  I achieved the ligand parameters from ANTECHAMBER that are usable for
>> GROMACS software.
>> After using this command line :
>>
>>  $AMBERHOME/exe/ambpdb -p lig.prmtop < lig.inpcrd > lig.pdb
>>
>> The pdb structure of ligand visualized with VMD and it was OK, but after
>> minimization step when I see em.gro and em.trr file in VMD I saw that the
>> structure of ligand in a protein is broken and a series of unusual bonds
>> are fromed.
>>
>>
>> Apparently all parameters are correct and I don't have any Warning or
>> Notes
>> in each steps but I don't know where the problem is in this stage.
>>
>> I'm really appreciate if you could help me,
>>
>> Regards,
>>
>> Yeganeh
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>