[gmx-users] extending simulation with grompp incorporating velocities

[Mark Abraham]

On 21/10/2011 4:51 PM, Chandan Choudhury wrote:
> On Fri, Oct 21, 2011 at 10:26 AM, Mark Abraham 
> <Mark.Abraham at anu.edu.au <mailto:Mark.Abraham at anu.edu.au>> wrote:
>
>     On 21/10/2011 3:25 PM, Chandan Choudhury wrote:
>
>
>         Dear gmx users,
>
>         A simulation was performed for 50 ns with
>
>         ; RUN CONTROL
>         integrator               = md
>         nsteps                   = 50000000
>         dt                       = 0.001
>         ; OUTPUT CONTROL
>         nstxout                  = 1000
>         nstvout                  = 1000
>         nstxtcout                = 0
>         nstlog                   = 100
>         nstenergy                = 100
>
>         The output produced were 0-50.edr, 0-50.trr, 0-50.log,
>         0-50.pdb state.cpt, state_prev.cpt. The simulation completed
>         normally.
>
>         After 50 ns, I intend to extend for 4 more ns, write the
>         trajectory file frequently with
>
>
>     Use tpbconv -extend. See
>     http://www.gromacs.org/Documentation/How-tos/Extending_Simulations
>
>
> I was aware with the tpbconv command. But while using the tpbconv 
> command, we cannot change the output frequency. If somehow the 
> trajectory writing frequency can be changed, it will solve my curiosity.

Ah. Well for a new .mdp, you need the combination of nsteps, init_step 
and the step number in the .cpt to all make mutual sense, and perhaps 
tinit, etc. also. gmxdump -cp may help here. Note that tinit and 
init_step refer to the whole simulation, not the start of any 
non-initial chunk.

Mark
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