[gmx-users] Error with equilibration of DPPC membrane with protein

Edvin Erdtman 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?
>> -Justin
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