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