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

[Neha]

So I would have to successively set tinit to the time of the last restart?

Can I ask why that doesn't seem to be a problem when I am simply switching
from saving every 10steps to every 100 steps? I am not at time zero then
either, but at 2ps and grompp and mdrun did not complain then.


Justin Lemkul wrote
> On Tue, Jul 2, 2013 at 1:23 PM, Neha <

> nshafique@

> > 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 .umaryland

>  | (410) 706-7441
> 
> 
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