[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:
> Hi
> 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?


> /Edvin
> 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


Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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