Hi JM,
> To all the users who have been testing the LIPID11 force field:
> I have been using LIPID11 with a POPC bilayer (128 lipids and a
> water/lipid ratio greater than 30), at 303 K with the Langevin
> thermostat (ntt = 3, gamma_ln = 1.0), with semi-isotropic coupling (ntp
> = 3), pressure in z of 1 atm (pres0 = 1, taup = 2.0)and a surface
> tension of 17 dynes/cm (csurften = 3, gamma_ten = 17), as recommended
> by Professor Ross Walker.
> However, after 50 ns of simulation, the area per lipid values have
> been ranging between 60 and 62 A2, far from the 64.3 A2 experimental
> values. What should I do? …
That's strange - we don't see that. See the attached figure. It's possible that 50ns is not enough time to equilibrate. I'd let it run to at least 100ns and see what changes. Depending on where you got your initial structure from it can take a long time for the are per lipid in these bilayers to converge. If you do ultimately see different results from us after 100ns or so it would be interesting to know the specific details of your system setup so we can try to reproduce it here.
All the best
Ross
/\
\/
|\oss Walker
---------------------------------------------------------
| Assistant Research Professor |
| San Diego Supercomputer Center |
| Adjunct Assistant Professor |
| Dept. of Chemistry and Biochemistry |
| University of California San Diego |
| NVIDIA Fellow |
|
http://www.rosswalker.co.uk |
http://www.wmd-lab.org/ |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
---------------------------------------------------------
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Received on Thu Jun 28 2012 - 13:00:02 PDT
