[gmx-users] Re: small tc-group

Peter C. Lai pcl at uab.edu
Fri Oct 12 15:36:24 CEST 2012

On 2012-10-12 04:40:35AM -0700, fciocco wrote:
> Thanks Peter for your reply
> actually, I did not think about that possibility because in the most
> windows, I have this small highly charged peptide out of the membrane.
> Moreover, in the last US windows, the peptide creates a defect and there are
> several water molecules inside the membrane. So, if I think about this fact,
> I associate the peptide with the SOL molecules, because of it charged
> nature...
> some questions come to my mind:
> If I'll have a simple charged aminoacid or a bigger charged peptide, the
> definition for the tc_groups that you proposed me, would be the same (i.e.
> peptide_membrane)? I think that it could be a little tricky to see. 

Yeah this will be size dependent. I went back and looked at Justin's 
KALP_15 tutorial and he appears to be able to run a separate tc-group
for a single continuous peptide of 15 residues.

My area of familiarity is with continuous membrane proteins averaging 
300-400 amino acids, and I use separate tc-groups for protein, membrane, and 
SOL_Ions. However, when I introduce small molecule ligands into the system, 
which are on the order of 10-15 heavy atoms per molecule, they are temperature 
coupled with water because: they are still much smaller than lipid acyl 
chains and there are very few of them compared to the number of water 
molecules in the system (never more than 1:200 ratio) so they do not 
contribute too much to sampling or distribution. If you are concerned 
about temperature coupling very small peptides or single AAs then try 
coupling them to water and see what happens. 

> I should be worried about the high temperature fluctuations if I choose the
> peptide as an individual tc_group.?
> Can this different elections of the tc_grps affect the final PMF profile?  

If you have significant temperature fluctuations they will, by definition...

Peter C. Lai			| University of Alabama-Birmingham
Programmer/Analyst		| KAUL 752A
Genetics, Div. of Research	| 705 South 20th Street
pcl at uab.edu			| Birmingham AL 35294-4461
(205) 690-0808			|

More information about the gromacs.org_gmx-users mailing list