[gmx-users] Minimization problem, again!

[liu xin]

Hello Andrea,

Thank you for your suggestion!

If my protein/membrane system has some clashes, how can I find them and
correct them, cause I am not very clear when you say "removed them". I
checked my starting structure with VMD many times, it seemed all right.
Could you please give me some further suggestions?

Thanks in advance!

On 12/15/05, andrea spitaleri <spitaleri.andrea at hsr.it> wrote:
>
> Hi
> I had a similar problem with protein/membrane system and I found that the
> starting structure was wrong. Precisly, there were few clashes between atoms
> of the protein with the membrane. Once removed them, the min worked fine.
> I hope this can help,
> Regards
>
> Andrea
>
> liu xin wrote:
>
> Dear GROMACS users,
>
> My minizization problem still got no resolvment, even I restarted from
> make hole, using different values for "hfm", I got almost the same message
> when I try to minimize my lipid/protein system.  so I send this mail again
> asking for help.
>
> I checked the output energy, after SD minimization with my lipid/protein
> system, found the values are abnormal:
>
> ##########################################################################
> Steepest Descents converged to machine precision in 15 steps,
> but did not reach the requested Fmax < 2000.
> Potential Energy  =            nan
> Maximum force     =            inf on atom 9614
> Norm of force     =            nan
> ##########################################################################
>
> Then I checked the em.log line by line, found there are two message:
>
> ##########################################################################
> Stepsize too small, or no change in energy.
> Converged to machine precision,
> but not to the requested precision Fmax < 2000
>
> Double precision normally gives you higher accuracy.
> You might need to increase your constraint accuracy, or turn
> off constraints alltogether (set constraints = none in mdp file)
> ##########################################################################
>
> Infact I did set "constraints = none" in mdp file, and I got the same
> result when changing the stepsize from 0.002 to 0.02. I searched this
> forum, somebody said it is because of bad start structure, so I restarted
> from makeing hole, using hfm = 5, 10, 10 then 100, 100, 150, but I still got
> almost the same result, except that the atom number of "Maximum force"
> varies, I am new to gromacs, I've been stuck into this problem for a week,
> could anybody give me some suggestions? Any suggestions will be highly
> appriciated!
>
> Thanks in advance!
>
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> --
> -------------------------------
> Andrea Spitaleri
> Dulbecco Telethon Institute
> c/o DIBIT Scientific Institute
> Biomolecular NMR, 1B4
> Via Olgettina 58
> 20132 Milano (Italy)
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