[gmx-users] Restrained EM and cut-offs

Ivano Eberini Ivano.Eberini at unimi.it
Tue Apr 30 09:29:06 CEST 2002

Dear GROMACS users,
I am trying to minimize a protein structure obtained by homology 
I used the following .mdp file:

cpp = /usr/bin/cpp
constraints = none
integrator = cg
nsteps = 250
emtol = 100
emstep = 0.00001
nstcomm = 1
ns_type = grid
rlist = 0.8
rcoulomb = 1.4
rvdw = 0.8
Tcoupl = no
Pcoupl = no
gen_vel = no

I have two questions:

1) If I use "define = -DPOSRES" and I prepared a posre.itp file, can I 
run a restrained (cg and steep) EM procedure or this is right just for 

2) I read this interesting mail by Bert de Groot, posted on December on 
gmx-users list:
"Only for special purposes (like for example a Normal Modes
type of calculation) you would need to minimize further, but then you
a) should not use a cut-off (because you get fluctuations in the energies
because of that and b) should probably move to double precision."

I installed a copy of GROMACS in double precision, but how can I run EM 
disabling cut-offs?

Thanks in advance.
Best regards,

Ivano Eberini

Ivano Eberini
Gruppo di Studio per la Proteomica e la Struttura delle Proteine
Dipartimento di Scienze Farmacologiche
Università degli Studi di Milano
Via G. Balzaretti, 9
20133 - Milano
Tel.: +390250318359-8304/-8359 Fax: +390250318284


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