[gmx-users] SD and CG EM!

[Marco Ceruso]

Hi Luciano
I haven't followed all your e-mails from the beginning
and people might have already said this.
I don't know which system you are using but the total
energy seems way off if you have a system in water.
In any case, I would start minimizing with steepest descent alone
(integrator = steep)  first,
and then move to a mixture of conjugate gradients and steepest descent
(integrator= cg and nstcgsteep =100)
the nstcgsteep is the frequency (in steps) that the minimization algorithm
will switch from cg to steepest descent.
I hope this helps
Marc

> -----Original Message-----
> From: gmx-users-admin at gromacs.org [mailto:gmx-users-admin at gromacs.org]On
> Behalf Of Luciano Tavares
> Sent: Thursday, November 20, 2003 4:55 PM
> To: gmx-users at gromacs.org
> Subject: [gmx-users] SD and CG EM!
>
>
>
>  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.
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> ##      Luciano Tavares da Costa * ltcosta at universiabrasil.net      ##
> ##           Laboratory of Theoretical Chemistry-DQ UFSCar          ##
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