RE: deformations in a cubic water box during equilibration in NAMD

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Fri Nov 03 2006 - 01:53:23 CST

Try doing two stages, the first at constant pressure until the volume is
steady, then at constant volume. Only free the protein in a CV simulation
after these two. The water density is probably too low if you start with
CV, hence the deformations.

-----Original Message-----
From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On Behalf
Of regafan_at_usc.es
Sent: Thursday, November 02, 2006 8:53 AM
To: namd-l_at_ks.uiuc.edu
Subject: namd-l: deformations in a cubic water box during equilibration in
NAMD

Hello,
I have problems in the equilibration of a protein using NAMD. I have
tried lots of trial&error and this is what I have seen.

-When I apply constant pressure and restraints in all the protein, the
water box is not deformed, but in the next step I cannot take off the
restraints because errors related to RATTLE appear.

-When I apply constant volume (flexibleCell no), the equilibration
ends without error but the water box is deformed (the vertices are not
squared, the walls are not rectiline,...)

-I tried also changing the way of heating the system (langevin off and
reassignFreq, reassignTemp, reassignIncr,...; langevin on,...), but no
changes.

I have seen that some people have had this problem, too, but I havent
found the solution. Can anybody help me?

Thanks a lot in advance!

Rebeca García
Post-doctoral researcher
Universidad de Barcelona

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