[gmx-users] Md continuation with cpt

[Justin A. Lemkul]

Anna Marabotti wrote:
> Dear gmx-users,
> since I'm sending my simulations to a system with a queue with a 
> wallclock time of 24 h, I necessarily have to simulate small parts of my 
> simulation, that I "stick" together at the end with trjconv. To continue 
> my simulations, I'm using the .cpt file. Here my settings concerning the 
> number of steps, dt etc. Since I started the full MD after 20 ps NVT and 
> 100 ps NPT I set the mdp file as:
>  
> integrator = md
> dt = 0.002
> nsteps = 2500000 (total 5 ns - the max time compatible with the 
> wallclock time)
> init_step = 70000 (the last step after NVT+NPT)

Is it?  120 ps/0.002 ps = 60000 steps.

<snip>

> Opened 1R3Afull20ns.edr as double precision energy file
> frame:      0 (index      0), t:    140.000        

Based on this output, frame 0 corresponds to a time of 140 ps, as set by your 
init_step * dt.

> Reading energy frame      2 time  300.000          
> Timesteps at t=200 don't match (60, 100)

It looks like the setting for nstenergy is causing frames to be written at 
integral multiples of 100 ps, rather than init_step + nstenergy.  So you have 
frame 0 at 140 ps, frame 1 at 200 ps, then 100-ps intervals until...

> Reading energy frame     50 time 5100.000          
> Timesteps at t=5100 don't match (100, 40)
>  

etc.

> Timesteps at t=5140 don't match (40, 60)
>  
> Timesteps at t=5200 don't match (60, 100)
> Reading energy frame    100 time 10000.000          
> Timesteps at t=10100 don't match (100, 40)
>  
> Timesteps at t=10140 don't match (40, 60)
>  
> Timesteps at t=10200 don't match (60, 100)
> Reading energy frame    150 time 14900.000          
> Timesteps at t=15100 don't match (100, 40)
>  
> Timesteps at t=15140 don't match (40, 60)
>  
> Timesteps at t=15200 don't match (60, 100)
> Last energy frame read 198 time 19600.000           
>  

All of these mismatches seem to agree with the above theory.  The difference is 
always 40 or 60, the remainder of some break between your value determined by 
init_step  and initial time of 140 ps.

> Found 199 frames.
>  
> gcq#131: "Royale With Cheese" (Pulp Fiction)
> I don't understand why there are so many mismatches in my file. Moreover 
> all but one are in the correspondence of the "junctions" I made between 
> two consecutive 5 ns runs. Does it depend on some settings regarding 
> init_step or dt or tinit in the .mdp file? Did I make correctly the 
> continuation? Could somebody help me to find the error?

Is there some reason you needed the trajectory to start at 140 (120?) ps? 
Usually a new trajectory is intitiated with init_step = 0.  Continuing a run 
using while still maintaining the previous ensemble does not necessarily need 
init_step > 0.

It is possible this is a bug related to nst*out/energy/log being writing every 
50000 steps and assuming init_step = 0 (i.e. writing at 100 ps rather than 240 
ps, based on your initial settings).  What version of Gromacs is this?

-Justin

> Many thanks in advance and best regards
> Anna
>  
> __________________________________________________________________
> Anna Marabotti, Ph.D.
> Laboratory of Bioinformatics and Computational Biology
> Institute of Food Science - CNR
> Via Roma, 64
> 83100 Avellino
> Phone: +39 0825 299651
> Fax: +39 0825 781585
> E-mail: amarabotti at isa.cnr.it <mailto:amarabotti at isa.cnr.it>
> Skype account: annam1972
> Web site: http://bioinformatica.isa.cnr.it/anna/anna.htm
>  
> "When a man with a gun meets a man with a pen, the man with the gun is a 
> dead man"
> (Roberto Benigni, about Roberto Saviano)
>  
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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