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

[Mark Abraham]

Stefano Meliga wrote:
> Hi again,
> 
> The energy minimization with conjugate gradient integrator still gives 
> me two warnings of the type:
> 
> t = 0.011 ps: Water molecule starting at atom 28122 can not be settled.
> Check for bad contacts and/or reduce the timestep.

OK I checked the code, and reporting a timestep is erroneous. Apologies 
for my misleading advice earlier. I filed a bugzilla about the message. 
It likely should read "Step 11: Water molecule..."

Nonetheless, the water at around 28122 may have had a serious problem 
that is worth checking out, lest something break later on in the simulation.

Mark

> My command lines are:
> 
> $grxdir/grompp -f 4AKEpreEMcg.mdp -po 4AKE_EMcg.mdp -c 4AKE_EMsteep.gro 
> -p 4AKEallHion.top -pp 4AKEpreEMsteep.top -o 4AKE_EMcg.tpr
> $grxdir/mdrun -s 4AKE_EMcg.tpr -o 4AKE_EMcg.trr -c 4AKE_EMcg.gro -e 
> 4AKE_EMcg.edr -g 4AKE_EMcg.log -v
> 
> This is my mdp file 4AKEpreEMcg.mdp:
> 
> title               =  4AKE_EMcg
> cpp                 =  /usr/bin/cpp
> define              =  -DFLEXIBLE
> constraints         =  none
> integrator          =  cg
> nsteps              =  1500
> nstlist             =  50
> ns_type             =  grid
> rlist               =  1.0
> rcoulomb            =  1.0
> rvdw                =  1.0
> ;
> ;       Energy minimizing stuff
> ;
> emtol               =  1.0
> emstep              =  0.01
> 
> 
> The minimization is successful but I don't see the meaning of this 
> timestep.
> 
> Thanks,
> 
> Stefano.
> 
> 
> Justin A. Lemkul ha scritto:
>>
>>
>> Stefano Meliga wrote:
>>> 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?
>>>
>>
>> Position restraints != bond contraints.  Using "constraints = 
>> all-bonds" will constrain the bond lengths, but not restrain the 
>> positions of the atoms.
>>
>> If you want to do position-restrained MD, you have to "define = 
>> -DPOSRES" (according to the #ifdef POSRES block in the topology, 
>> assuming you made one automatically from pdb2gmx).  Using position 
>> restraints in EM doesn't serve much of a purpose in my mind, unless 
>> you really need to preserve the exact initial configuration; it may in 
>> fact prevent your system from converging if some bad geometry is being 
>> held in place.
>>
>> -Justin
>>
>>> 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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