[gmx-users] charmm c36 lipids
t.piggot at soton.ac.uk
Fri Oct 1 17:27:29 CEST 2010
For a POPC bilayer then both your and my files produce the same tpr's
(checked both with gmxcheck and gmxdump). This is pleasing as I not only
scripted the conversions but did some parts by hand! I shall check the
other lipids to make sure that there are no discrepancies in these.
Also for my files I have included the bonded and non-bonded parameters
with parameters from CHARMM27 so as to allow simulations in water and
with proteins. I want to re-check these before contributing the
forcefield to the website, so it will probably be next week before I
upload it. Just to let you know I will use your lipids.rtp as it has the
atoms in separate charge groups so as to avoid having to use
-nochargegrp with pdb2gmx, whilst mine doesn't. I hope this is fine with
Pär Bjelkmar wrote:
> Hi Tom,
> great do that! If there're no discrepancies and you have tested it we should probably put your version among the user contributions. Let me know how it goes!
>> Hi Par,
>> I have a working version of the CHARMM36 lipids that I converted myself,
>> which I am fairly confident is correct. I shall check your parameters
>> against my ones to confirm everything is the same and report back to the
>> list. I don't see anything which would not work for your script as there
>> are not any major changes to the forcefield in CHARMM36.
Dr Thomas Piggot
University of Southampton, UK.
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