Subject: Molecular Dynamics Vol, Perssure & Density issues

From: ssr97lrc <[email-masked]>
Date: Sat, 10 Jun 2000 19:43:36 +0100 (BST)

dear all,

i'd like to run a series of md experiments at various
temperatures; 298 and 398k using gromacs2

in both cases the pressure of the solvent bath is set to 1 atm at the
start of unrestrained md but averages -1.4 atm during the 298k run and
10.7atm during the 398k run, density fluctuates around 1.0 kg/l in both
runs.

>from a paper by daggett et al i have gleaned that densities should be are
altered in md solvent bath simulations to compensate for increased
temperature ie a 498k simulation would be conducted with density ~0.8kg/l,
i think. that calculation is referenced to a paper i cannot obtain at present.

****so at what density should a 398k simulation be conducted at and how
is that calculated considering water must stay in liquid phase?

will summarise

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/=\Mr. Lee R. Cooper MSc,           P.E.D.A.L, Dept.of//=\
=// Comp. Science, University of Reading, Whiteknights\=//
//=\ PoBox 225, Reading, Berkshire. RG6 6AY (UK)       //=\
  °¤ø,¸¸,ø¤°`´°¤ø,¸¸,ø¤°`´°¤ø,¸¸,ø¤°`´°¤ø,¸¸,ø¤°`´°¤ø,¸¸,ø¤°`

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From: ssr97lrc <[email-masked]>
Date: Sat, 10 Jun 2000 18:52:06 +0100 (BST)

dear all,

could anyone name a free modelling package for win98 or redhat linux
which does all of the following things;

o handles pdb files cleanly
o has full atom typing capabilities
o allows you to sketch/build covalently modified cys, lys or n-term 
residues
o select & clean (with conjugate grad min) the modified residue
o (re)name the added atoms

of course msi's cerius2 software does three of these things but it does
not fulfil the first criterion

¤ø,¸¸,ø¤°`´°¤ø,¸¸,ø¤°`´°¤ø,¸¸,ø¤°`´°¤ø,¸¸,ø¤°`´°¤ø,¸¸,ø¤°`
/=\Mr. Lee R. Cooper Bsc(Hons) MSc, P.E.D.A.L, Dept.of//=\
=// Comp. Science, University of Reading, Whiteknights\=//
//=\ PoBox 225, Reading, Berkshire. RG6 6AY (UK)       //=\
\=// Tel +44 (0)118 987 5123 x7645 (0915-1700)|Fax     \=//
 °¤ø,¸¸,ø¤°`´°¤ø,¸¸,ø¤°`´°¤ø,¸¸,ø¤°`´°¤ø,¸¸,ø¤°`´°¤ø,¸¸,ø¤°`