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

[Stefano Meliga]

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.

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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