[gmx-users] -pbc nojump failure

[Irem Altan]

I think the problem is that I can’t seem to start from an unfragmented structure. I start from the .pdb file, where the protein is a whole, and end up with a .tpr file that is fragmented. The interesting thing is, this did not happen with version 4.6.5 (I now use 5.1.2). Do I have to do something extra while preparing the simulation system? 

Here is what I’m currently doing:

gmx pdb2gmx -f xxxx.pdb -o box.gro -p topol.top         (then I choose amber99sb and tip4pew)
gmx solvate -cp box.gro -cs tip4p -p topol.top -o box_h2o.gro
gmx grompp -f ions.mdp -c box_h2o.gro -o ions.tpr -p topol.top
gmx genion -s ions.tpr -p topol.top -o ions.gro -neutral -conc 0.05  (I choose to replace the solvation waters, SOL)
gmx -f minim.mdp -p topol.top -c ions.gro -o em.tpr
gmx mdrun -v -deffnm em
gmx grompp -f nvt.mdp -p topol.top -c em.gro -o nvt_water_frozen.tpr

Then I run the simulation with mdrun. The .mdp files are almost identical to Justin’s files from the Lysozyme tutorial. In the above steps, is there something that seems like it could cause the fragmentation issue? 

Best,
Irem

> On Mar 31, 2016, at 11:54 AM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
> 
> No! You can't do that, because fitting will cause the PBC and the
> coordinates to mismatch. So 'nojump' after that will for sure screw up the
> coordinates. Check the trjconv workflow on the Gromacs site.
> 
> Cheers,
> 
> Tsjerk
> On Mar 31, 2016 14:23, "Francesco Carbone" <fra.carbone8 at gmail.com> wrote:
> 
>> You could try to fit first (-fit rot+trans) and fix pbc (-pbc nojump)
>> later.
>> 
>> Cheers,
>> 
>> Fra
>> 
>> On 31 March 2016 at 05:45, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
>> 
>>> Hi Irem,
>>> 
>>> Check the structure in nvt_water_frozen.tpr:
>>> 
>>> gmx editconf -f nvt_water_frozen.tpr -o ref.pdb
>>> 
>>> Cheers,
>>> 
>>> Tsjerk
>>> On Mar 31, 2016 00:04, "Irem Altan" <irem.altan at duke.edu> wrote:
>>> 
>>>> Hi,
>>>> 
>>>> I am simulating a protein in its unit cell. I use the original .pdb
>> file
>>>> as an input, so the initial molecule is not fragmented. At the end of
>> the
>>>> simulation, I generate a .pdb file containing the trajectory of the
>>> protein
>>>> as follows:
>>>> 
>>>> gmx trjconv -f nvt_water_frozen.trr -s nvt_water_frozen.tpr -dt 20 -pbc
>>>> nojump -o prot.pdb
>>>> 
>>>> Despite the fact that I use -pbc nojump, I still get all the
>> coordinates
>>>> wrapped into the unit cell, and therefore the protein fragmented. What
>>>> could be wrong? (I use GROMACS 5.1.2)
>>>> 
>>>> Best,
>>>> Irem
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