[gmx-users] T-coupling groups

[jampani srinivas]

Dear Zuzana,

Recently i have done similar selection, I have got this error only when i
miss some atoms or when i have some atoms in both groups. I would suggest
you to check your groups carefully or you can make indexes for these
selections in VMD and check whether you are missing some atoms from both
groups.

Srinivs.


On Thu, Mar 18, 2010 at 4:55 PM, Zuzana Benkova <Zuzana.Benkova at savba.sk>wrote:

> Dear GROMACS users,
> I have checked the mails in archive which deal with the problem I am facing
> but did not find the answer what I do wrong.
>
> I want to compile a PEO chain centered in box of 2900 water molecules.
>
> In my md.mdp the relevant section is as follows
> Tcoupl              =  nose-hoover
> tc-grps             =  PEO  SOL
> tau_t               =  0.1  0.1
> ref_t               =  50   50
> gen_vel             =  yes
> gen_temp            =  50   50
>
> I have generated an index file where I have defined the PEO group. The [
> SOL ] group contains 129-8828 atoms and the [ PEO ] contains 1-128atoms.
> This matches with the gro file. I tried to prepare a tpr file using
>
> grompp -f md.mdp -c PEO18_2900TIP3P_opt.gro -n PEO18_2900TIP3P.ndx  -p
> topol.top -o PEO18_2900TIP3P_50K
>
> and got message
>
> Program grompp, VERSION 4.0.3
> Source code file: readir.c, line: 1050
>
> Fatal error:
> 16 atoms are not part of any of the T-Coupling groups
>
> I tried the compilations with 4.0.3 and 4.0.5 versions but the message was
> the same.
>
>
>  I would be really thankful for an advice which can move me further. Thank
> you in advance.
>
> Zuzana
>
>
>
>
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-- 
*********************************************
J. Srinivasa Rao Ph.D.
Post-doctoral Research Associate
C/o Prof. Luis R Cruz Cruz
Computational Biophysics Group
Department of Physics
Drexel University
3141 Chestnut St
Philadelphia, PA 19104, USA.
Ph:  Off:     215-895-1989
       Mob:  704-706-4191
Web:http://jsrao.web.officelive.com/default.aspx
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