[gmx-users] Re: solution molecules cannot be set by mdrun after neutralization

[Stefano Meliga]

My integrator is "steep", which should perform EM.
This is my mdp file:

title               =  4AKE_PREMsteep
cpp                 =  /usr/bin/cpp
define              =  -DFLEXIBLE
constraints         =  all-bonds
integrator          =  steep
nsteps              =  500
nstlist             =  10
ns_type             =  grid
rlist               =  1.0
rcoulomb            =  1.0
rvdw                =  1.0
DispCorr = no
;
;       Energy minimizing stuff
;
emtol               =  1.0
emstep              =  0.01

I learnt from the tutorials (s-peptide) that in order to do a position 
restrained MD the I have to set the constraints (all-bonds in this case).
Is that incorrect? Is it valid for EM as well?

Thank you for your advice,
Stefano.


Mark Abraham ha scritto:
> Stefano Meliga wrote:
>> Hi again,
>>
>> I've tryed to perform the same preprocessing and EM steps without 
>> distance constraints and the situation improves a lot.
>> I get no warnings in the steepest descent EM and only one molecule 
>> cannot be set in the conjugate gradient EM.
>> Can you see the reason?
>
> Yes. You're not doing EM. "t = 0.011 ps:" is a big clue. Choose your 
> integrator in your .mdp file better.
>
> Also, as Justin suggests, please be careful with the 
> constraint/restraint terminology.
>
> Mark
>
>> Thanks,
>> Stefano.
>>
>> Stefano Meliga ha scritto:
>>> Hi everybody,
>>>
>>> I neutralized my system with the commands:
>>>
>>> $grxdir/grompp -f dummy.mdp -po dummyout.mdp -c 4AKEallHsol.gro -p
>>> 4AKEallH.top -pp 4AKEallHsol_pre.top -o 4AKEallHsol.tpr
>>> $grxdir/genion -s 4AKEallHsol.tpr -o 4AKEallHion.gro -p
>>> 4AKEallHsol_pre.top -np 4 -pname NA+ -g -pot 4AKEallHion.pdb -nname
>>> CL-
>>> (adding the atoms to the solution SOL)
>>>
>>> I renamed the files to keep track of the different topology files:
>>>
>>> mv 4AKEallHsol_pre.top 4AKEallHion.top
>>> mv "#4AKEallHsol_pre.top.1#" 4AKEallHsol_pre.top
>>>
>>> I run an all-bonds position restraint steepest descent EM:
>>>
>>> $grxdir/grompp -f 4AKEprePREMsteep.mdp -po 4AKE_PREMsteep.mdp -c
>>> 4AKEallHion.gro -p 4AKEallHion.top -pp 4AKEallHion_out.top -o
>>> 4AKEallHion.tpr
>>> $grxdir/mdrun -s 4AKEallHion.tpr -o 4AKE_PREMsteep.trr -c
>>> 4AKE_PREMsteep.gro -e 4AKE_PREMsteep.edr -g 4AKE_PREMsteep.log -v
>>>
>>> mdrun exits successfully but displays the warning:
>>> t = 0.011 ps: Water molecule starting at atom 17223 can not be settled.
>>> Check for bad contacts and/or reduce the timestep.
>>>
>>> In the gro file atom 17223 is an oxigen of the solution
>>>
>>> Going further with my simulation i run a all-bonds position restrained
>>> conjugate gradient EM:
>>>
>>> $grxdir/grompp -f 4AKEprePREMcg.mdp -po 4AKE_PREMcg.mdp -c
>>> 4AKE_PREMsteep.gro -p 4AKEallHion_out.top -pp 4AKEallH_PREMsteep.top
>>> -o 4AKEallH_PREMsteep.tpr
>>> $grxdir/mdrun -s 4AKEallH_PREMsteep.tpr -o 4AKE_PREMcg.trr -c
>>> 4AKE_PREMcg.gro -e 4AKE_PREMcg.edr -g 4AKE_PREMcg.log -v
>>>
>>> but get the fatal error:
>>>
>>> Source code file: constr.c, line: 136
>>>
>>> Fatal error:
>>> Too many LINCS warnings (2200)
>>>
>>> And some of this warnings are again solution's molecules that cannot 
>>> be set.
>>> May the problem be related to the ions added to neutralise the system?
>>> mdrun was not showing this problem with the non-neutral system in
>>> input.
>>>
>>> Thanks a lot,
>>> Stefano
>>>
>>>   
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