From: Dimitar V Pachov (dpachov_at_brandeis.edu)
Date: Thu Mar 11 2010 - 09:09:56 CST
----- "tillmann utesch" <tillmann.utesch_at_mail.tu-berlin.de> wrote:
| From: "tillmann utesch" <tillmann.utesch_at_mail.tu-berlin.de>
| To: namd-l_at_ks.uiuc.edu
| Sent: Thursday, March 11, 2010 7:01:06 AM GMT -05:00 US/Canada Eastern
| Subject: namd-l: high pressure
| Hi all,
| I run a NPT simulation of an enzyme on a SAM coated gold surface.
| During the simulation all gold atoms were fixed to their positions.
It is not a good idea at all to run NPT with any positional constraints. Pressure is controlled by volume scaling. Fixed coordinates introduce artifacts and certain frequency wave propagation/fluctuations that are not desired. You cannot say that your system samples appropriately the equilibrium NPT ensemble in that case.
| The total system is neutrally charged, but the head-groups of the
| monolayers are positively and the gold atoms are negatively charged.
| So the charges are not able (gold) or limited (SAM) in moving.
| The simulations are very stable, but the the pressure is fluctuating
| around a very high value.
What is "very high"? How large are the fluctuations? Instantaneous pressure tends to fluctuate a lot, but your average should be around the externally specified value.
| For the pressure control I used the Langevin
| piston method. Forces between fixed atoms were ignored and for the
| electrostatic interactions I used the PME summation.
| Exclusion of gold and SAM atoms of the pressure calculations did not
| change the very high pressure in the system.
| What shall I do now? Is the high pressure a result of the high charge
| density in the SAM and the gold? How can a modify my system to get
| normal pressure values?
What is "normal"?
I do not know why you want to fix the gold atoms, but it would be much better (but not prefect) to put (small) positional harmonic restraints which will allow at least some spacial degrees of freedom. Or you could try NVT.
| Tillmann Utesch
| Institut für Chemie, Max-Volmer-Laboratorium
| TU Berlin, PC 14
| Straße des 17. Juni 135
| D-10623 Berlin
| Tel. +49-(0)30-314-26389
-- ======================================================== Dimitar V Pachov PhD Candidate Physics & Biochemistry Department Phone: (781) 736-2326 Brandeis University, MS 057 Email: dpachov_at_brandeis.edu ========================================================
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