[gmx-users] Re: hp.mdp

[Graham Smith]

Hi 

I'm not sure exactly how big your system is, but 
the message you posted on Monday morning contains the lines 
> POPC   106 
and 
> ... number of coordinates in coordinate file (popc_b4em.gro,204786)

If this is still the system you are using, then, since popc
contains 52 atoms, hp1=1, hp2=52*106=5512. 

And if you want the extra z-forces, s1=5513 (first water atom?),
s2=204786 (last water atom?). 

However, if you don't want any of this, then you can set hp1, hp2, s1
and s2 all to 0 and it will still run. (I forgot to say that in the
documentation, sorry again).

BTW If you really have so much water, then it's more than you need.
Peter Tieleman's original file has only 2460 water molecules (rather
than 66424) for 128 lipids. 
You can reduce it by making the box smaller in z before running
genbox. (the box is at the end of a .gro file). 

G 

########################################################################

Dr. Graham R. Smith,
Biomolecular Modelling Laboratory,
Cancer Research UK,
44 Lincoln's Inn Fields,
London WC2A 3PX,
U.K.
Tel: +44-(0)20 7269 3348
email: graham.smith at cancer.org.uk
URL: http://www.bmm.icnet.uk/~smithgr