[gmx-users] (no subject)

[Justin A. Lemkul]

JMandumpal wrote:
>  
> I think, setting tc groups = system    will solve this issue.

Bad idea.  Treating the protein and the surrounding solvent together will lead
to temperature differences between the two groups, such that the overall system
will have the correct temperature, but the protein and solvent will be at
different temperatures - certainly non-physical!

There is a reason that grompp suggests using Protein/Non-Protein...

-Justin

> 
> On Thu, 17 Jul 2008 Justin A.Lemkul wrote :
>  >For warnings/errors, etc. please check the archive and wiki before 
> posting.  I just responded to a similar issue a few days ago:
>  >
>  >http://www.gromacs.org/pipermail/gmx-users/2008-June/034786.html
>  >
>  >-Justin
>  >
>  >alkasrivastava at iitb.ac.in wrote:
>  >>Hi all
>  >>I have installed gromacs 3.3.3 in one of my 32 machine fedora core 2.
>  >>so check i tried to to do speptide tutorial in
>  >>/usr/local/gromacs/share/gromacs/tutor/speptide
>  >>
>  >>But when i m running grompp for position restraint with the command
>  >>grompp -f pr -o pr -c after_em -r after_em -p speptide
>  >>
>  >>i get the following warning
>  >>
>  >>  WARNING 1 [file aminoacids.dat, line 1]:
>  >>  T-Coupling group Protein has fewer than 10% of the atoms (191 out of
>  >>  2741)
>  >>  Maybe you want to try Protein and Non-Protein instead?
>  >>
>  >>I tried to change SOL with non protein but getting the same warning. 
> is it
>  >>ok to go further with this warning
>  >>
>  >>When i did grompp for full MD with the command
>  >>
>  >>grompp -v -f full -o full -c after_pr -p speptide
>  >>
>  >>again i m getting the same warning
>  >>
>  >>WARNING 1 [file aminoacids.dat, line 1]:
>  >>  T-Coupling group Protein has fewer than 10% of the atoms (191 out of
>  >>  2741)
>  >>  Maybe you want to try Protein and Non-Protein instead?
>  >>
>  >>
>  >>I tried to change SOL with non protein but getting the same warning.
>  >>
>  >>I don't know what to do now and how can i overcome this, if anyone could
>  >>help me.
>  >>
>  >>Thanks
>  >>
>  >>ALKA
> 
> 
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-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================


-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================