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

[Justin A. Lemkul]

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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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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