[gmx-users] Error with equilibration of DPPC membrane with protein
Justin A. Lemkul
jalemkul at vt.edu
Wed Apr 1 14:43:23 CEST 2009
Edvin Erdtman wrote:
> We have tried with no cutoff, as I have written in former emails, but
> that was when we got trouble with LINCS warnings. We then thought that
> we could try to continue remove lipids in the compression-steps to get
> rid of that LINCS warnings, and to have a stable system!
> Is it maybe the protein that is the problem - need to be more minimized?
Maybe yes, maybe no. If I remember your original post, you are doing the
annealing with Nose-Hoover as the thermostat. IIRC, N-H does not respond well
to changes in temperature (it fluctuates a lot). Maybe try your protocol using
a weak coupling scheme, Berendsen or V-rescale?
> Justin A. Lemkul wrote:
>> Justin A. Lemkul wrote:
>>> Edvin Erdtman wrote:
>>>> Hi again
>>>> I don't know if you were aware of it, but I have commented some
>>>> Justin's questions further down in the e-mail (my last e-mail wasn't
>>>> only a thank-email). Since it took so long, and other similar
>>>> discussions are still running I thought you have missed my comments
>>>> (see below).
>>>> Now we have tried with a Calpha-P cutoff of 5 Å (i.e. perl
>>>> inflategro.pl em1/confout.gro 0.97 DPPC 5 em2/input.gro 5
>>>> em2/area.dat), and position restraints on the protein, I have also
>>>> merged Cl and SOL in the same temp group, but it does not seem to
>>>> work anyway. We still get the LINCS warnings.
>>> Why are you using a cutoff during the compression phase? You will
>>> continue to delete lipids! I have never had a problem if I scale up
>>> by a factor of 4, with a 1.4-nm cutoff, then compress by a factor of
>>> 0.95 (with no cutoff).
>>> Maybe that will make a difference?
Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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