[gmx-users] Continuing simulation with velocities and positions of equilibrated run and after modifying .mdp

[Mark Abraham]

Hi,

A) yes
B) inspect the energies reported immediately after the restart for identity
C) please upgrade to a less prehistoric version

Mark

On Mon, 17 Oct 2016 00:32 Bappa Ghosh <ab54741 at gmail.com> wrote:

> Hello All,
>
> I have a  polymer chain of N=50. I equilibrate (NVT) the polymer for nsteps
> = 50000 at T= 295K keeping only the N=1 positional restrained  .
> After finishing the equilibration run, the production run is to be started
> lifting the positional restrain and applying a pull force on N=1 along
> Z-direction.
>
> My questions
> (A) Can I use the state.cpt file of the completed equilibration run to
> start my production from the same velocities and positions ?
> In this case, I have to modify .mdp file in two places for production run-
> (1) to lift the positional restrain on N=1 , I need to remove "define =
> -DPOSRES_N1".
> (2) to apply the pull force on N=1 ,     pull= constant_force
>                                                                pull_group1=
> N1
>                                                                pull_dim= N
> N Y
>                                                                pull_k1 = 5
>
> (B) Is there a way to check that I am starting  from the same velocities
> and positions  of the last equilibration frame ?
> I am using GROMACS-4.5.5 (single precision).
>
> Thank you in advance.
>
> Best regards,
> Bappa Ghosh
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