[gmx-users] Error with equilibration of DPPC membrane with protein
edvin.erdtman at oru.se
Wed Apr 1 14:25:58 CEST 2009
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?
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?
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