[gmx-users] peptide MD

[Daniel Larsson]

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

+46-18-471 4006 (phone)
+46-18-511 755  (fax)
http://xray.bmc.uu.se/~larsson
larsson at xray.bmc.uu.se