Re: [gmx-users] PBC after energy minimization

2020-05-02 Thread Justin Lemkul




On 5/1/20 9:29 AM, John Whittaker wrote:

Hi Mohamed,


Hello everybody,

In order to solve the PBC at the end I use the command:

*gmx trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_noPBC.xtc -pbc mol *

followed by:

*gmx trjconv -s md_0_1.tpr  -f md_noPBC.xtc -o md_noPBC.pdb*


I want to solve this problem after the energy minimization but I don't
have
.xtc file to use it as I do at the end.

How can I solve this problem after the energy minimization ?

You're saying that your energy minimization does not produce a trajectory
(a .trr or .xtc file)?

If that's the case, you just have to instruct GROMACS to periodically
write to a trajectory file using options in the .mdp file (namely,
nstxout). Take a look at:

http://manual.gromacs.org/documentation/2018/user-guide/mdp-options.html

Under the section "output control" you will find what you are looking for.


"Trajectories" from energy minimization are generally unreadable as the 
interval of saved frames is uneven. During EM, a frame is only written 
when the energy goes down, which is not necessarily every possible 
frame. I also seem to recall that there is never XTC output from EM, 
even if requested, because it's rather pointless. Maybe that has changed.


-Justin

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Virginia Tech Department of Biochemistry
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Re: [gmx-users] PBC after energy minimization

2020-05-01 Thread John Whittaker
Hi Mohamed,

> Hello everybody,
>
> In order to solve the PBC at the end I use the command:
>
> *gmx trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_noPBC.xtc -pbc mol *
>
> followed by:
>
> *gmx trjconv -s md_0_1.tpr  -f md_noPBC.xtc -o md_noPBC.pdb*
>
>
> I want to solve this problem after the energy minimization but I don't
> have
> .xtc file to use it as I do at the end.
>
> How can I solve this problem after the energy minimization ?

You're saying that your energy minimization does not produce a trajectory
(a .trr or .xtc file)?

If that's the case, you just have to instruct GROMACS to periodically
write to a trajectory file using options in the .mdp file (namely,
nstxout). Take a look at:

http://manual.gromacs.org/documentation/2018/user-guide/mdp-options.html

Under the section "output control" you will find what you are looking for.

- John

>
> Thanks,
> Mohamed
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> posting!
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John Whittaker
Ph.D. Candidate
Department of Mathematics and Computer Science
Freie Universit├Ąt Berlin

+49 0160 936 04221

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