[gmx-users] emtol in a water box

Tanos tccf at taurus.ime.eb.br
Thu Oct 31 20:29:56 CET 2002

    Hi users,
    When peforming a energy minimization of a dimeric protein (formed by 02
monomeric units of 442 residues) in a water's box, I noted that GROMACS
never converges to emtol values under about 418 Kj/mol.nm. So, I decided to
run the "speptide in a water's box" example of the tutorial to check this. I
noticed that the em.mdp file of this example uses emtol of 2000 than, I
tryed to test values under 2000. GROMACS converged until the value of emtol
of about 205. When I tryed 100, the calculation stopped and output the
message: "stepsize too small converged to machine precision". So, once the
same problem happens with the tutorial example, I would like to ask if a
emtol of 2000 or 1000 could be fine to a minimization of a protein in a
water's box.
    I am trying to perform the minimization until about 41,8 because in a
energy minimization in vacum this is the ideal value, but I am not sure if
it would be the same to a water's box. I am also looking for examples in
literature but it would be very nice if someone answer this question
    Best whises,
    Tanos C. C. Franca.

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