[gmx-users] Dynamics

Thu Jan 26 09:47:34 CET 2017

Dear Rahul,

I really don’t think you understand the concept of pbc in molecular simulations. Please read up on the concept in appropriate literature.

Kind regards,
Erik
______________________________
Erik Marklund, PhD
Marie Skłodowska Curie INCA Fellow
Department of Chemistry – BMC
Uppsala Universtity
erik.marklund at kemi.uu.se<mailto:erik.marklund at kemi.uu.se>

On 26 Jan 2017, at 09:25, RAHUL SURESH <drrahulsuresh at gmail.com<mailto:drrahulsuresh at gmail.com>> wrote:

Thank you

But if I am extending my simulation with protein outside the box, then
there will not be any effect of water molecules right.?

On Thu, 26 Jan 2017 at 1:25 PM, <jkrieger at mrc-lmb.cam.ac.uk<mailto:jkrieger at mrc-lmb.cam.ac.uk>> wrote:

Hi Rahul,

The protein being out of the box is not a problem except for visualisation

and some analysis (e.g. RMSD). For continuing the simulation, it is a

completely normal consequence of having periodic boundaries and you

shouldn't worry about it. You can then fIx the protein for visualisation

and analysis separately to running. See

http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

To continue the simulation just use mdrun as normal but with the -cpi

flag. If you want more time than you originally set the mdp to ask for

then use tpbconv (gmx convert_tpr in gromacs 5 and later). See

http://www.gromacs.org/Documentation/How-tos/Extending_Simulations

Best wishes

James

Hi mark

I want to extend it for another 50ns. At 100ns protein is out of the box.

Now is t possible to apply boundary conditions and extend.?

On Wed, 25 Jan 2017 at 11:12 PM, Mark Abraham <mark.j.abraham at gmail.com>

wrote:

Hi,

On Wed, 25 Jan 2017 18:00 RAHUL SURESH <drrahulsuresh at gmail.com> wrote:

from production output of a monomer for 100ns, there s a instability

in

the

structure from 83ns to 100ns.

Many things could be going on here...

Also .gro file shows, the protein is out of

the cube.

Mdrun doesn't care. There's infinitely many equivalent representations

of a

periodic system.

http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

gmx make_ndx -f md.gro -o index.ndx

trjconv -f md.xtc -s md.tpr -n index.ndx -pbc mol -ur compact -center

-o

outputfile.xtc

I used the above commands to bring the protein to the center of the

box.

gmx trjconv -f outputfile.xtc -s md.tpr -o newmd.trr

And using the above command, extracted a trr file.

Now can I extend this job with this trr file as it is or should i give

any

periodic boundary conditions or should take the conformer structure at

80ns

and run for another 50ns?

None of this is needed. See

http://www.gromacs.org/Documentation/How-tos/Extending_Simulations

Whether it makes sense to try to repeat or extend or go back to the

start

and try to fix something depends on what the "instability" is, and what

is

causing it.

Mark

waiting for your valuable note.

--

*Regards,*

*Rahul Suresh*

*Research Scholar*

*Bharathiar University*

*Coimbatore*

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