On Mar 4, 2008, at 10:52, Rigden, LucianeVMello wrote:
Dear users,
Trying to perform a MD for a peptide 12aa long.
Following the tutorial for peptides MD:
http://www.gromacs.org/documentation/reference/online/speptide.html
everything seems fine till I reach PR MD.
First I get a warning for grompp:
WARNING 1 [file aminoacids.dat, line 1]:
T-Coupling group Protein has fewer than 10% of the atoms (201 out of
5150)
Maybe you want to try Protein and Non-Protein instead?
WARNING 2 [file aminoacids.dat, line 1]:
T-Coupling group K+ has fewer than 10% of the atoms (5 out of 5150)
Maybe you want to try Protein and Non-Protein instead?
The reason for the warning is that temperature coupling for very
small subsets of the system is ill-defined. Usually it is best to use
as few temperature coupling groups as possible; one for the solute
(protein or similar) and one for the solvent (water, ions, etc.).
Read here for more information:
http://wiki.gromacs.org/index.php/Thermostats
I thought, I need to change
tc-grps = Protein SOL K+
; Time constant (ps) and reference temperature (K) =
tau-t = 0.1 0.1 0.1
ref-t = 300 300 300
TO
; Groups to couple separately =
tc-grps = Protein Non-protein
; Time constant (ps) and reference temperature (K) =
tau-t = 0.1 0.1
ref-t = 300 300
but, when trying to run grompp again 01 warning is still there
(once it is
related to the protein group).
Not really sure if using non-protein for the sol and ion is really
helping (!!??)
WARNING 1 [file aminoacids.dat, line 1]:
T-Coupling group Protein has fewer than 10% of the atoms (201 out of
5150)
You have a system with quite a lot of water compared to the size of
the protein.
I downloaded all the files for the tutorial exercise (speptide - a
19aa long) and I get the same
problem. However this warning seems not to be too important, since
there is no
mention to it at the tutorial.
The main difference between my system and the tutorial one is the
non-charge
zero for the system. For that I have added 5 K+ to it.
But, of course, for the tutorial I run step by step with no
alteration.
But, when running MD:
mdrun -v pr.mdp -s topol.tpr
Step 0, time 0 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max inf (between atoms 1 and 2) rms inf
bonds that rotated more than 30 degrees:
and MD crashes.
And again I get this error for my system and for speptide (the
tutorial exercise).
I am using gromacs 3.3 and have tried
0: GROMOS96 43a1 force field and
6: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
I am wondering why I am having so much trouble, even when running
the tutorial.
Any help would be much appreciated.
Thanks in advance,
Luciane
Dr Luciane Vieira de Mello
School of Biological Sciences
Room 2.20, Life Science Building
Tel:(+44) 151 795 5140
FAX:(+44) 151 794 5130
University of Liverpool
Crown St.,Liverpool L69 7ZB, U.K.
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---
Daniel Larsson
Molecular Biophysics group
Department of Cell and Molecular Biology
Uppsala University
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