[gmx-users] peptide MD

[Rigden, LucianeVMello]

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?

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)
 

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.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20080304/16b9d1b1/attachment.html>