[gmx-users] RE: Is non-linear data output/storage possible?

[Justin Lemkul]

On Tue, Jul 2, 2013 at 1:23 PM, Neha <nshafique at wesleyan.edu> wrote:

> Hi,
>
> So the commands are:
>
> grompp -f 10step.mdp -p dppc_bilayer.top -o 10step.tpr -c dppc_bilayer.gro
>
> mdrun -nt 4 -s 10step.tpr -c nonlinear.gro -e nonlinear.edr -x
> nonlinear.xtc
> -o nonlinear.trr -g nonlinear.log -cpo nonlinear.cpt -rdd 2.5
>
> grompp -f 100step.mdp -c 10step.tpr -p dppc_bilayer.top -o 100step.tpr -t
> nonlinear.cpt
>
> mdrun -nt 4 -s 100step.tpr -c nonlinear.gro -e nonlinear.edr -x
> nonlinear.xtc -o nonlinear.trr -g nonlinear.log -cpi nonlinear.cpt -cpo
> nonlinear.cpt -rdd 2.5
>
> Up till this point the output is what I would expect. However now I try to
> use the 10step mdp again in order to save it every ten time steps -
>
>  grompp -f 10step.mdp -c 100step.tpr -p dppc_bilayer.top -o 10step.tpr -t
> nonlinear.cpt
>
> mdrun -nt 4 -v -s 10step.tpr -c nonlinear.gro -e nonlinear.edr -x
> nonlinear.xtc -o nonlinear.trr -g nonlinear.log -cpi nonlinear.cpt -cpo
> nonlinear.cpt -rdd 2.5
>
> And at this mdrun I get WARNING: This run will generate roughly
> 186617909559164928 Mb of data
>
> starting mdrun 'DPPC BILAYER'
> 100 steps, infinite ps (continuing from step 1000,     20.0 ps).
>
>
> This is the saving every 10 steps mdp file, the hundred step is identical
> except steps is a 1000 and nstxout is 100.
>
> ; VARIOUS PREPROCESSING OPTIONS =
> title                    = Martini
> cpp                      = /usr/bin/cpp
>
> ; RUN CONTROL PARAMETERS =
> integrator               = md
> ; start time and timestep in ps =
> tinit                    = 0.0
>

This is your problem.  You're no longer at t = 0.  The checkpoint file
specifies some time in the future, so grompp thinks you're going backwards
in time and thinks you're going to generate infinite data by doing so.
Then mdrun gets confused, because it thinks you're trying to go backwards
as well, from step 1000 to step 100.  Proper use of tinit and init_step in
the .mdp file should alleviate this problem.

-Justin

-- 

==========================================

Justin A. Lemkul, Ph.D.
Postdoctoral Associate

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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