[gmx-users] Deformation of bio-polymer

[V.V.Chaban]

What is the problem to set EACH pressure components using anisotropic
pressure coupling, see MDP file?

Remember that barostats do not like non-equilibrium MD.

If the condensed matter system has already been equilibrated under the
desired conditions, I would just do pulling in the NVT ensemble.
Otherwise, your coupling
 times must correlate with pulling rates.





On Mon, Jun 15, 2015 at 5:05 AM, mohammad mostafa
<mohammad.mostafa2015 at yahoo.com> wrote:
> Dear All users and developersI want to study the pressure effects on the mechanical properties of a bio-polymer (that is, Young modulus or stress-strain curve) by uni-axial deformation of simulation box in z-direction via all-atom MD simulation. For this purpose, the simulation cell was first equilibrated at desired pressure under NPT ensemble to obtain the true density. The final cell from equilibration run was used as input box to be deformed in its z-direction using 0.001 nm/ps deformation rate. Deformation simulation was also performed in NPT ensemble, where the pressure was controlled semi-isotropically via Berendsen barostat. Here, my question is that how I can set the pressure in non-deformed directions (i.e., x and y) and deformed direction (i.e., z). For example, if I want to deform the cell at 100 atm, how is the value of pressure in x, y and z direction during deformation simulation? I studied the Manual of GROMACS in detail, but it did not help me to solve this is
>  sue.
> Your suggestions are highly appreciated.
> Mohammad
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.