[gmx-users] Reducing density using -vdwd option for a new solvent in the system

[Justin A. Lemkul]

shivangi nangia wrote:
> Hello Justin and everybody,
> 
> I created a system of charged polyhistdine, counter anions and just 1 
> DHB molecule is a box without making any change in the vdwradii.dat file.
> This system does not energy minimize, it stops with the same message:
> 
> Stepsize too small, or no change in energy.
> Converged to machine precision,
> but not to the requested precision Fmax < 10
> 
> Double precision normally gives you higher accuracy.
> 
> What can be done to fix this problem?
> 

Take some time to search the Gromacs website and the mailing list archive.  You 
would have undoubtedly found either this:

http://www.gromacs.org/Documentation/Errors#Stepsize_too_small.2c_or_no_change_in_energy._Converged_to_machine_precision.2c_but_not_to_the_requested_precision

or the hundreds of other messages that post this message, which is neither a 
problem, nor an error, per se.

> 
> The part of  DHB itp file is:
> [ moleculetype ]
> ; Name nrexcl
> DHB      3
> 
> [ atoms ]
> ;   nr      type  resnr resid  atom  cgnr   charge     mass
>      1        OM     1  DHB     OAA     1   -0.567  15.9994
>      2         C     1  DHB     CAH     1    1.135  12.0110
>      3        OM     1  DHB     OAD     1   -0.568  15.9994
>      4         C     1  DHB     CAK     2   -0.004  12.0110
>      5       CR1     1  DHB     CAG     2    0.004  12.0110
>      6        HC     1  DHB     HAG     2    0.033   1.0080
>      7         C     1  DHB     CAI     2    0.141  12.0110
>      8        OA     1  DHB     OAB     2   -0.179  15.9994
>      9         H     1  DHB     HAB     2    0.005   1.0080
>     10       CR1     1  DHB     CAE     3    0.000  12.0110
>     11        HC     1  DHB     HAE     3    0.000   1.0080
>     12       CR1     1  DHB     CAF     3    0.000  12.0110
>     13        HC     1  DHB     HAF     3    0.000   1.0080
>     14         C     1  DHB     CAJ     4    0.082  12.0110
>     15        OA     1  DHB     OAC     4   -0.113  15.9994
>     16         H     1  DHB     HAC     4    0.031   1.0080
> 
> 

This topology looks like complete junk.  Earlier I provided you a link to PRODRG 
tips and told you there was an article referenced there you should read.  I 
certainly hope you will do so.  If you run a simulation with a lousy topology, 
you'll get lousy results.  Either the system will be unstable or the results 
will be completely untrustworthy.

> 
> 
> 
> If I have the water/methanol or water:methanol in the system as the 
> solvent, the system runs fine.
> 

Well, what's the solvent in the case of the unstable system?  Just because some 
other systems appear stable does not mean anything else will be.

-Justin

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

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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