|
Thank you Tsjerk;
I followed your advice, and it looks
working well.
Cheers,
Hiromichi
----- Original Message -----
Sent: Wednesday, June 14, 2006
8:13 PM
Subject: Re: [gmx-users] Error:
Not enough ref_t and tau_t values
Hi Hiromichi,
It is likely that you have some groups
which are not covered by "Protein" and "Other". You can use "Protein" and
"Non-Protein" in stead. But make sure that the two groups correspond to two
distinct groups in your system. You may run into trouble if you have some
non-standard residue in your protein which will end up in the "Non-Protein"
group.
Cheers,
Tsjerk
On 6/14/06, Hiromichi
Tsurui <[EMAIL PROTECTED]>
wrote:
Dear all;
I am trying to calculate the binding free energy of an
MHC-molecule and a peptide by thermodynamic integration method. The system
contains binding domain of MHC molecule, a peptide presented on it,
water-molecules (about 13,000), and ions (Na+ and Cl- at
PBS-concentration).
After energy minimization, I tried to equilibrate the
system with the mdp-file as follows, and an error-message appeared as
such;
"Fatal error.
Not enough ref_t and tau_t
values."
How should I change the conditions
?
Many thanks for your
help.
cpp
=
/lib/cpp
define
=
integrator
=
md
tinit
=
0.0
dt
= 0.002
nsteps
= 100000
nstcomm
=
1
nstxout
=
50000
nstvout
=
50000
nstfout
=
0
nstlog
=
10000
nstenergy
=
250
nstxtcout
=
10000
xtc_precision
=
1000
xtc_grps
=
Protein
energygrps
= Protein
other
nstlist
=
5
ns_type
=
grid
pbc
=
xyz
rlist
=
0.9
coulombtype
=
Reaction-Field
epsilon_r
=
78.0
rcoulomb
=
1.4
vdw-type
=
Cut-off
rvdw
=
1.4
tcoupl
= Berendsen
tc-grps
=
Protein
other
ref_t
= 300
300
tau_t
= 0.1
0.1
pcoupl
=
Berendsen
tau_p
=
1.0
compressibility
=
4.6e-5
ref_p
=
1.0
gen-vel
=
yes
gen-temp
=
300
gen-seed
=
$RANDOM
constraints
=
all-bonds
Hiromichi Tsurui MD, PhD
Dept.
Pathology,
Juntendo
University
Phone:81-3-5802-1039
Fax:81-3-3813-3164
[EMAIL PROTECTED]
_______________________________________________
gmx-users
mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please
don't post (un)subscribe requests to the list. Use the
www interface or
send it to [EMAIL PROTECTED].
Can't
post? Read http://www.gromacs.org/mailing_lists/users.php
--
Tsjerk A.
Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology
Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336
_______________________________________________
gmx-users mailing
list
gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please
don't post (un)subscribe requests to the list. Use the
www interface or
send it to [EMAIL PROTECTED]
Can't post? Read
http://www.gromacs.org/mailing_lists/users.php
|
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
