[gmx-users] SD and CG EM!

[Martina Bertsch, PhD]

Hi, Luciano.

I use:

integrator          = cg 
nsteps              = 10000
ns_type             = grid
nstlist             = 10
rlist               = 1.0
rcoulomb            = 1.0
rvdw                = 1.0

emtol               = 1000 
emstep              = 0.01
nstcgsteep          = 100 (comment out with sd)

If you have no lipid, SOL or ions, then when running pdb2gmx for the protein, you should select the GROMOS ff43b1 vacuum forcefield.
 
Best,

Martina

Luciano Tavares wrote:

> Hi Martina Bertsch and gmx-users,
>
> Thanks for advise...
>
> Well, I'm sorry my persistence. I have tried to do the protocol that
>Martina had adviced me. However, I have performed EM just putting only the
>protein, without pbc such as below:
>
>title               =  EM
>cpp                 =  /lib/cpp
>integrator          =  cg   ; initially with steep
>nsteps              =  1000
>nstcgsteep          =  0.01
>emtol               =  27000 ; starting with 50000, 40000 and after 30000
>emstep              =  0.001
>
>pbc                 =  no
>nstcomm             =  1
>ns_type             =  simple
>nstlist             =  0
>rlist               =  0.0
>rcoulomb            =  0.0
>rvdw                =  0.0
>Tcoupl              =  no
>Pcoupl              =  no
>gen_vel             =  no
>
>But, the message have appeared again in this stage, with emtol = 27000
>kJ*mol^-1*nm^-1:
>
>Step 9, E-Pot = 1.0114848125e+06, Fmax =  5.40031e+05, atom = 1668
>Step 10, E-Pot = 1.0114861250e+06, Fmax =  5.19963e+05, atom = 1863
>Negative w:  -5.214692788374e+23
>z=  -1.151546032128e+12
>gpa=   6.963870543712e+11, gpb=   2.653018202711e+12
>a=   0.000000000000e+00, b=   1.102683569454e-10
>EpotA=   1.011486125000e+06, EpotB=   1.011651562500e+06
>Negative number for sqrt encountered (-521469278837438404362240.000000)
>Terminating minimization
>
>I guess it wouldn't be some kind of mistake with the structure,
>because I have already performed a pdb2gmx command with no problems. What
>the hinted of the parameters (or terms) above?!
>
>Well, very very thanks in advance...
>
>Luciano
>
>PS: I'm sorry, my last messages were with problems in the format.
>######################################################################
>##      Luciano Tavares da Costa * ltcosta at universiabrasil.net      ##
>##           Laboratory of Theoretical Chemistry-DQ UFSCar          ##
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