[gmx-users] T-coupling groups

[Zuzana Benkova]

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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