Subject: temperature control in AMBER / NAMD

From: Lubos Vrbka <[email-masked]>
Date: Wed, 04 Dec 2002 12:08:24 +0100

dear CCLers,

i'm trying to "translate" AMBER input to NAMD, but i experienced 
following "problem":

tempi = 300.0, temp0 = 300.0, ntt = 1, tautp = 0.5,
can be "translated" into NAMD as

temperature 300
rescaletemp 300
rescalefreq 500

or using tcouple, tcoupletemp, tcouplefile and tcouplecol parameters. is 
the former "translation" sufficient and will it do what i expect (i.e. 
hold the temperature at 300K using rescaling forces to 300K every 500th 
step)? it seems to me that NAMD doesn't support berendsen temperature 
coupling algorithm used in AMBER (ntt = 1), just berendsen pressure bath 
coupling, that is not useful for me at this time since i do just vacuum 
simulation.

in case i'll use
tcouple 
	on
tcoupletemp 
300
tcouplefile 
name.pdb
tcouplecol 
b

what value should i set as the beta-factor in the pdb file? i'm not 
experienced with this, i'd expect using value 1 for all atoms should be 
ok. could anyone help me, please?

TIA
l.vrbka

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Lubos Vrbka
National Centre for Biomolecular Research
Masaryk university, Brno, Czech Republic

[email-masked]
http://www.chemi.muni.cz/~shnek
tel. +420 5 4112 9508
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